Morphometric Shape Analysis of Corpus Callosum in Children With Down Syndrome

Down syndrome (DS) is characterized by varying degrees of mental retardation and delay in neurocognitive functions. Herein, we analyzed the morphometric shape of the corpus callosum (CC) in children with DS. Twenty-three DS cases underwent magnetic resonance imaging and have grossly normal CC, and 23 control group cases were included in this retrospective study (2012-2020). The CC was obtained from T2-weighted mid-sagittal images, and certain anatomical points were marked on the CC. Statistical geometric shapes and deformations of CC were evaluated for both groups. The age range of patients with DS and control group was 6 to 42 months. A statistically significant difference was found in the shape of CC between the groups (P < .001). Deformation was most evident in the splenium in the DS group.

Quantifying dysmorphologies of the neurocranium using artificial neural networks

BACKGROUND

Craniosynostosis, a congenital condition characterized by the premature fusion of cranial sutures, necessitates objective methods for evaluating cranial morphology to enhance patient treatment. Current subjective assessments often lead to inconsistent outcomes. This study introduces a novel, quantitative approach to classify craniosynostosis and measure its severity.

METHODS

An artificial neural network was trained to classify normocephalic, trigonocephalic, and scaphocephalic head shapes based on a publicly available dataset of synthetic 3D head models. Each 3D model was converted into a low-dimensional shape representation based on the distribution of normal vectors, which served as the input for the neural network, ensuring complete patient anonymity and invariance to geometric size and orientation. Explainable AI methods were utilized to highlight significant features when making predictions. Additionally, the Feature Prominence (FP) score was introduced, a novel metric that captures the prominence of distinct shape characteristics associated with a given class. Its relationship with clinical severity scores was examined using the Spearman Rank Correlation Coefficient.

RESULTS

The final model achieved excellent test accuracy in classifying the different cranial shapes from their low-dimensional representation. Attention maps indicated that the network's attention was predominantly directed toward the parietal and temporal regions, as well as toward the region signifying vertex depression in scaphocephaly. In trigonocephaly, features around the temples were most pronounced. The FP score showed a strong positive monotonic relationship with clinical severity scores in both scaphocephalic (ρ = 0.83, p < 0.001) and trigonocephalic (ρ = 0.64, p < 0.001) models. Visual assessments further confirmed that as FP values rose, phenotypic severity became increasingly evident.

CONCLUSION

This study presents an innovative and accessible AI-based method for quantifying cranial shape that mitigates the need for adjustments due to age-specific size variations or differences in the spatial orientation of the 3D images, while ensuring complete patient privacy. The proposed FP score strongly correlates with clinical severity scores and has the potential to aid in clinical decision-making and facilitate multi-center collaborations. Future work will focus on validating the model with larger patient datasets and exploring the potential of the FP score for broader applications. The publicly available source code facilitates easy implementation, aiming to advance craniofacial care and research.

Statistical shape analysis of the lentiform nucleus of children of different age groups: a retrospective study

The basal nuclei are important during infancy because of the significant development of motor skills. The main aim of this study was to evaluate the shape differences of the lentiform nucleus between different age and gender groups. A total of 126 children's axial magnetic resonance image series were included in the presented study. These images were grouped between 1 and 5 yr old. Right and left lentiform nuclei are marked with selected landmarks using TPSDIG v2.04. Statistical shape analyses were examined by a Generalized Procrustes Analysis. Our results showed that there was no statistically significant difference in lentiform nucleus shape between genders. However, there was a difference between the shapes of the right and left lentiform nuclei between the 1-yr and 5-yr age groups. These results demonstrated the shape changes in the lentiform nucleus during the first 5 yr of life. Further clinical studies based on our results may be used to gather more detailed information about movement disorders and neuronal development.

Chewing asymmetry in dogs: Exploring the importance of the fossa masseterica and first molar teeth morphology

Dogs are animals with strong bite force. This strong bite mechanism has led to significant changes in the skeletal system such as fossa masseterica. It can be thought that one side is used more than the other side in chewing and is related to the preference of using the same side's hand, eye and foot. In the study, directional asymmetry and fluctuating asymmetry, which occurs as a result of chewing asymmetry, were examined on the first molar teeth and the fossa masseterica in 85 dog mandibles including a wide diversity of morphotypes. The association of high PC1 values for directional asymmetry with a pronounced cranial index, as evident in breeds like Pekingese, Pomeranian and Bulldog, indicates a potential evolutionary or selective breeding trend favouring brachycephaly. On the contrary, guardian breeds like the German shepherd and Bernese mountain dog, which typically require strong jaws for their roles, showcased reduced PC1 values, which might be related to their functional morphology. Similarly, the PCA results for the first molar teeth shape variations also highlighted the influence of cranial shape, with boxer dogs displaying notably higher PC1 values. The fluctuating asymmetrical distributions provided valuable insights into individualistic variations. Interestingly, no specific breed distribution trend was observed for these asymmetries, indicating a more individual-based variation rather than breed-based. It is essential to note that while these results provide valuable insights, further studies are required to understand the underlying causes better. Factors like genetic variations, developmental processes, dietary habits and external environmental factors could play pivotal roles in these observed morphological differences.

Geometric morphometric evaluation of mandibles of four sheep breeds: Bardoka, İvesi, Polish Mountain sheep and Turcana

The enduring relationship between humans and domestic sheep has evolved over millennia, showcasing diverse uses such as meat, milk, wool, leather and fur, shaped by geographical, historical, cultural and social factors. The sheep breeds discussed include the Ivesi from Southeastern Anatolia, known for its varied animal products; the resilient Turcana breed of Romania; Kosovo's Bardoka, valued for its triple-purpose characteristics; and Poland's Polish Mountain Sheep, uniquely utilized for milk production in cheese making. Sheep, with their enduring relationship with humans and significant economic importance, have attracted scientific interest in morphometric studies of their mandibles, yielding valuable data applicable across various fields including basic anatomy, veterinary clinical anatomy, zooarchaeology and veterinary forensic medicine. Traditional morphometric studies rely on statistical methods to compare length, depth and angular ratios between anatomical formations, often highlighting differences between specific points but not fully revealing shape variations between distinct groups. Geometric morphometric analysis has emerged as a preferred method in recent years, enabling shape analyses using coordinate data from various imaging techniques, facilitating a comprehensive examination of mandibular morphometrics among sheep breeds across different countries. This study involved four sheep breeds from different countries, namely İvesi from Turkey, Bardoka from Kosovo, Polish Mountain Sheep from Poland and Turcana from Romania, with a total of 70 mandibles sourced from various veterinary faculties. Mandibular photographs were meticulously captured, focusing on the right side of mandible pairs and placing landmarks and semi-landmarks along the entire edge, enabling geometric morphometric analysis using tpsUtil, tpsDig2 and MorphoJ software. The analysis included principal component analysis, canonical variate analysis and discriminant function analysis for pairwise comparisons, facilitating a comprehensive examination of mandibular shape variations among the different sheep breeds. Using geometric morphometric methods, this study analysed mandibles from four distinct sheep breeds sourced from different countries, revealing notable variations in regions such as the ramus mandibula, angulus mandibula and incisive areas, attributed to genetic, geographical and dietary influences, highlighting the importance of continued research to better comprehend these shape differences.

Morphological changes in the cerebellum during aging: evidence from convolutional neural networks and shape analysis

The morphology and function of the cerebellum are associated with various developmental disorders and healthy aging. Changes in cerebellar morphology during the aging process have been extensively investigated, with most studies focusing on changes in cerebellar regional volume. The volumetric method has been used to quantitatively demonstrate the decrease in the cerebellar volume with age, but it has certain limitations in visually presenting the morphological changes of cerebellar atrophy from a three-dimensional perspective. Thus, we comprehensively described cerebellar morphological changes during aging through volume measurements of subregions and shape analysis. This study included 553 healthy participants aged 20-80 years. A novel cerebellar localized segmentation algorithm based on convolutional neural networks was utilized to analyze the volume of subregions, followed by shape analysis for localized atrophy assessment based on the cerebellar thickness. The results indicated that out of the 28 subregions in the absolute volume of the cerebellum, 15 exhibited significant aging trends, and 16 exhibited significant sex differences. Regarding the analysis of relative volume, only 11 out of the 28 subregions of the cerebellum exhibited significant aging trends, and 4 exhibited significant sex differences. The results of the shape analysis revealed region-specific atrophy of the cerebellum with increasing age. Regions displaying more significant atrophy were predominantly located in the vermis, the lateral portions of bilateral cerebellar hemispheres, lobules I-III, and the medial portions of the posterior lobe. This atrophy differed between sexes. Men exhibited slightly more severe atrophy than women in most of the cerebellar regions. Our study provides a comprehensive perspective for observing cerebellar atrophy during the aging process.

New insights into morphological adaptation in common mole-rats (Cryptomys hottentotus hottentotus) along an aridity gradient

Morphological adaptation is the change in the form of an organism that benefits the individual in its current habitat. Mole-rats (family Bathyergidae), despite being subterranean, are impacted by both local and broad-scale environmental conditions that occur above ground. Common mole-rats (Cryptomys hottentotus hottentotus) present an ideal mammalian model system for the study of morphological variation in response to ecology, as this species is found along an aridity gradient and thus can be sampled from geographically non-overlapping populations of the same species along an environmental longitudinal cline. Using the mass of five internal organs, ten skeletal measurements and 3D morphometric analyses of skulls, we assessed the morphology of wild non-breeding individuals from five common mole-rat populations in South Africa. We found that the body mass and mean relative mass of the spleen and kidneys in arid populations was larger, and individuals from arid regions possessed shorter legs and larger inter-shoulder widths compared to individuals from mesic regions. Additionally, arid populations demonstrated greater skull depth, and shape change of features such as angular processes of the lower jaw than mesic individuals, indicating that these distinct geographic populations show differences corresponding to the aridity gradient, potentially in response to environmental factors such as the variation in food sources found between different habitats, in addition to different soil compositions found in the different regions. Arid populations potentially require a stronger jaw and neck musculature associated with mastication to chew xeric-adapted plants and to dig through hard soil types, whereas mesic populations excavate through soft, looser soil and may make use of their front limbs to aid the movement of soils when digging. Aridity influences the morphology of this species and could indicate the impact of environmental changes on speciation and mammalian skull morphology.

Assessing Postoperative Motor Risk in Insular Low-Grade Gliomas Patients: The Potential Role of Presurgery MRI Corticospinal Tract Shape Measures

BACKGROUND

Insular low-grade gliomas (LGGs) are surgically challenging due to their proximity to critical structures like the corticospinal tract (CST).

PURPOSE

This study aims to determine if preoperative CST shape metrics correlate with postoperative motor complications in insular LGG patients.

STUDY TYPE

Retrospective.

POPULATION

42 patients (mean age 40.26 ± 10.21 years, 25 male) with insular LGGs.

FIELD STRENGTH/SEQUENCE

Imaging was performed using 3.0 Tesla MRI, incorporating T1-weighted magnetization-prepared rapid gradient-echo, T2-weighted space dark-fluid with spin echo (SE), and diffusional kurtosis imaging (DKI) with gradient echo sequences, all integrated with echo planar imaging.

ASSESSMENT

Shape metrics of the CST, including span, irregularity, radius, and irregularity of end regions (RER and IER, respectively), were compared between the affected and healthy hemispheres. Total end region radius (TRER) was determined as the sum of RER 1 and RER 2. The relationships between shape metrics and postoperative short-term (4 weeks) and long-term (>8 weeks) motor disturbances assessing by British Medical Research Council grading system, was analyzed using multivariable regression models.

STATISTICAL TESTING

Paired t-tests compared CST metrics between hemispheres. Logistic regression identified associations between these metrics and motor disturbances. The models were developed using all available data and there was no independent validation dataset. Significance was set at P < 0.05.

RESULTS

Short-term motor disturbance risk was significantly related to TRER (OR = 199.57). Long-term risk significantly correlated with IER 1 (OR = 59.84), confirmed as a significant marker with an AUC of 0.78. Furthermore, the CST on the affected side significantly had the greater irregularity, larger TRER and RER 1, and smaller span compared to the healthy side.

DATA CONCLUSION

Preoperative evaluation of TRER and IER 1 metrics in the CST may serve as a tool for assessing the risk of postoperative motor complications in insular LGG patients.

LEVEL OF EVIDENCE

2 TECHNICAL EFFICACY: Stage 2.

Orbital shape in sheep and goats with sex and breed factors

The purpose of this study was to identify the dimorphic structures of the orbita based on breed and sex factors through shape analysis across species. Additionally, the study aimed to ascertain the variability between the two species. A total of 86 (51 sheep-Akkaraman [Ak] and Morkaraman [Mk], 35 goats-Hair [Hr] and Honamlı [Hm]) skulls were used in the study. It was decided to designate 36 landmarks to represent the orbit's edge. In the principal component analysis, 68 PCs were calculated. It was determined that PC1, PC2 and PC3 explained the total variance in morphology by 26.909%, 16.147% and 13.616%, respectively. According to the cross-validation results, the goats were grouped with 95% (Hm: 100%, Hr: 90%), while the sheep were grouped with 56% (Ak: 50%, Mk: 63%). Therefore, dimorphism among goat breeds on orbita shape was more pronounced compared to sheep. In the discriminant function analysis of the sex groups, Procrustes and Mahalanobis distance values in goats were 0.04425425 (p < 0.0001) and 5.3733 (p = 0.9550), in sheep 0.03513424 (p < 0.0001) and 7.1003 (p = 0.9414), respectively, was detected. According to the cross-validation results, in terms of sex, goats were correctly grouped at a rate of 74% (F: 73%; M: 75%) and sheep breeds were correctly grouped at a rate of 72% (F: 77%; M: 66%). Factors such as habitat selection, breeding behaviours and ecological environment may show anatomical differences within breeds as well as between breeds. Therefore, various measurement techniques are used to reveal these differences. As a result, it is thought that the study will contribute to many disciplines, especially taxonomy and zooarchaeology, by analysing the shape of the orbita of sheep and goat breeds, the domestication of which dates back to ancient times, and revealing the similarities and differences between species and according to sex.

MR-based spatiotemporal anisotropic atrophy evaluation of hippocampus in Alzheimer's disease progression by multiscale skeletal representation

Increasing evidence has shown a higher sensitivity of Alzheimer's disease (AD) progression by local hippocampal atrophy rather than the whole volume. However, existing morphological methods based on subfield-volume or surface in imaging studies are not capable to describe the comprehensive process of hippocampal atrophy as sensitive as histological findings. To map histological distinctive measurements onto medical magnetic resonance (MR) images, we propose a multiscale skeletal representation (m-s-rep) to quantify focal hippocampal atrophy during AD progression in longitudinal cohorts from the Alzheimer's Disease Neuroimaging Initiative (ADNI). The m-s-rep captures large-to-small-scale hippocampal morphology by spoke interpolation over label projection on skeletal models. To enhance morphological correspondence within subjects, we align the longitudinal m-s-reps by surface-based transformations from baseline to subsequent timepoints. Cross-sectional and longitudinal measurements derived from m-s-rep are statistically analyzed to comprehensively evaluate the bilateral hippocampal atrophy. Our findings reveal that during the early AD progression, atrophy primarily affects the lateral-medial extent of the hippocampus, with a difference of 1.8 mm in lateral-medial width in 2 years preceding conversion (p < .001), and the medial head exhibits a maximum difference of 3.05%/year in local atrophy rate (p = .011) compared to controls. Moreover, progressive mild cognitive impairment (pMCI) exhibits more severe and widespread atrophy in the head and body compared to stable mild cognitive impairment (sMCI), with a maximum difference of 1.21 mm in thickness in the medial head 1 year preceding conversion (p = .012). In summary, our proposed method can quantitatively measure the hippocampal morphological changes on 3T MR images, potentially assisting the pre-diagnosis and prognosis of AD.

A landmark-free analysis of the pelvic girdle in Sulawesi ricefishes (Adrianichthyidae): How 2D and 3D geometric morphometrics can complement each other in the analysis of a complex structure

Geometric morphometrics (GM) enable the quantification of morphological variation on various scales. Recent technical advances allow analyzing complex three-dimensional shapes also in cases where landmark-based approaches are not appropriate. Pelvic girdle bones (basipterygia) of Sulawesi ricefishes are 3D structures that challenge traditional morphometrics. We hypothesize that the pelvic girdle of ricefishes experienced sex-biased selection pressures in species where females provide brood care by carrying fertilized eggs supported by elongated pelvic fins ("pelvic brooding"). We test this by comparing pelvic bone shapes of both sexes in species exhibiting pelvic brooding and the more common reproductive strategy "transfer brooding," by using landmark-free 2D and 3D GM, as well as qualitative shape descriptions. Both landmark-free approaches revealed significant interspecific pelvic bone variation in the lateral process, medial facing side of the pelvic bone, and overall external and internal wing shape. Within pelvic brooders, the three analyzed species are clearly distinct, while pelvic bones of the genus Adrianichthys are more similar to transfer brooding Oryzias. Female pelvic brooding Oryzias exhibit prominent, medially pointing tips extending from the internal wing and basipterygial plate that are reduced or absent in conspecific males, Adrianichthys and transfer brooding Oryzias, supporting our hypothesis that selection pressures affecting pelvic girdle shape are sex-biased in Sulawesi ricefishes. Furthermore, both sexes of pelvic brooding Oryzias have overall larger pelvic bones than other investigated ricefishes. Based on these differences, we characterized two reproductive strategy- and sex-dependent pelvic girdle types for Sulawesi ricefishes. Morphological differences between the investigated pelvic brooding genera Adrianichthys and Oryzias provide additional evidence for two independent origins of pelvic brooding. Overall, our findings add to a better understanding on traits related to pelvic brooding in ricefishes and provide a basis for upcoming studies on pelvic girdle function and morphology.

Effects of hypertension on subcortical nucleus morphological alternations in patients with type 2 diabetes

Objectives

Type 2 diabetes mellitus(T2DM) and hypertension(HTN) are common comorbidities, and known to affect the brain. However, little is known about the effects of the coexisting HTN on brain in T2DM patients. So we aim to investigate the impact of HTN on the subcortical nucleus morphological alternations in T2DM patients.

Materials & methods

This work was registered by the clinicaltrials.gov (grant number NCT03564431). We recruited a total of 92 participants, comprising 36 only T2DM patients, 28 T2DM patients with HTN(T2DMH) and 28 healthy controls(HCs) in our study. All clinical indicators were assessed and brain image data was collected for each participant. Voxel-based morphometry(VBM), automatic volume and vertex-based shape analyses were used to determine the subcortical nucleus alternations from each participant's 3D-T1 brain images and evaluate the relationship between the alternations and clinical indicators.

Results

T2DMH patients exhibited volumetric reduction and morphological alterations in thalamus compared to T2DM patients, whereas T2DM patients did not demonstrate any significant subcortical alterations compared to HCs. Furthermore, negative correlations have been found between thalamic alternations and the duration of HTN in T2DMH patients.

Conclusion

Our results revealed that HTN may exacerbate subcortical nucleus alternations in T2DM patients, which highlighted the importance of HTN management in T2DM patients to prevent further damage to the brain health.

Fine scale hippocampus morphology variation cross 552 healthy subjects from age 20 to 80

The cerebral cortex varies over the course of a person's life span: at birth, the surface is smooth, before becoming more bumpy (deeper sulci and thicker gyri) in middle age, and thinner in senior years. In this work, a similar phenomenon was observed on the hippocampus. It was previously believed the fine-scale morphology of the hippocampus could only be extracted only with high field scanners (7T, 9.4T); however, recent studies show that regular 3T MR scanners can be sufficient for this purpose. This finding opens the door for the study of fine hippocampal morphometry for a large amount of clinical data. In particular, a characteristic bumpy and subtle feature on the inferior aspect of the hippocampus, which we refer to as hippocampal dentation, presents a dramatic degree of variability between individuals from very smooth to highly dentated. In this report, we propose a combined method joining deep learning and sub-pixel level set evolution to efficiently obtain fine-scale hippocampal segmentation on 552 healthy subjects. Through non-linear dentation extraction and fitting, we reveal that the bumpiness of the inferior surface of the human hippocampus has a clear temporal trend. It is bumpiest between 40 and 50 years old. This observation should be aligned with neurodevelopmental and aging stages.

A novel geometry-based analysis of hippocampal morphometry in mesial temporal lobe epilepsy

Hippocampal volumetry is an essential tool in researching and diagnosing mesial temporal lobe epilepsy (mTLE). However, it has a limited ability to detect subtle alterations in hippocampal morphometry. Here, we establish and apply a novel geometry-based tool that enables point-wise morphometric analysis based on an intrinsic coordinate system of the hippocampus. We hypothesized that this point-wise analysis uncovers structural alterations not measurable by volumetry, but associated with histological underpinnings and the neuropsychological profile of mTLE. We conducted a retrospective study in 204 individuals with mTLE and 57 age- and gender-matched healthy subjects. FreeSurfer-based segmentations of hippocampal subfields in 3T-MRI were subjected to a geometry-based analysis that resulted in a coordinate system of the hippocampal mid-surface and allowed for point-wise measurements of hippocampal thickness and other features. Using point-wise analysis, we found significantly lower thickness and higher FLAIR signal intensity in the entire affected hippocampus of individuals with hippocampal sclerosis (HS-mTLE). In the contralateral hippocampus of HS-mTLE and the affected hippocampus of MRI-negative mTLE, we observed significantly lower thickness in the presubiculum. Impaired verbal memory was associated with lower thickness in the left presubiculum. In HS-mTLE histological subtype 3, we observed higher curvature than in subtypes 1 and 2 (all p < .05). These findings could not be observed using conventional volumetry (Bonferroni-corrected p < .05). We show that point-wise measures of hippocampal morphometry can uncover structural alterations not measurable by volumetry while also reflecting histological underpinnings and verbal memory. This substantiates the prospect of their clinical application.

Left ventricular anatomy in obstructive hypertrophic cardiomyopathy: beyond basal septal hypertrophy

AIMS

Obstructive hypertrophic cardiomyopathy (oHCM) is characterized by dynamic obstruction of the left ventricular (LV) outflow tract (LVOT). Although this may be mediated by interplay between the hypertrophied septal wall, systolic anterior motion of the mitral valve, and papillary muscle abnormalities, the mechanistic role of LV shape is still not fully understood. This study sought to identify the LV end-diastolic morphology underpinning oHCM.

METHODS AND RESULTS

Cardiovascular magnetic resonance images from 2398 HCM individuals were obtained as part of the NHLBI HCM Registry. Three-dimensional LV models were constructed and used, together with a principal component analysis, to build a statistical shape model capturing shape variations. A set of linear discriminant axes were built to define and quantify (Z-scores) the characteristic LV morphology associated with LVOT obstruction (LVOTO) under different physiological conditions and the relationship between LV phenotype and genotype. The LV remodelling pattern in oHCM consisted not only of basal septal hypertrophy but a combination with LV lengthening, apical dilatation, and LVOT inward remodelling. Salient differences were observed between obstructive cases at rest and stress. Genotype negative cases showed a tendency towards more obstructive phenotypes both at rest and stress.

CONCLUSIONS

LV anatomy underpinning oHCM consists of basal septal hypertrophy, apical dilatation, LV lengthening, and LVOT inward remodelling. Differences between oHCM cases at rest and stress, as well as the relationship between LV phenotype and genotype, suggest different mechanisms for LVOTO. Proposed Z-scores render an opportunity of redefining management strategies based on the relationship between LV anatomy and LVOTO.

The language-related cerebro-cerebellar pathway in humans: a diffusion imaging-based tractographic study

Background

The cerebellum and cerebral cortex form the most important cortico-cerebellar system in the brain. However, diffusion magnetic resonance imaging (MRI)-based tractography of the connecting white matter between the cerebellum and cerebral cortex, which support language function, has not been extensively reported on. This work aims to serve as a guideline for facilitating the analysis of white matter tracts along the language-related cerebro-cerebellar pathway (LRCCP), which includes the corticopontine, pontocerebellar, corticorubral, rubroolivary, olivocerebellar, and dentatorubrothalamic tracts.

Methods

The LRCCP templates were developed via processing the high-resolution, population-averaged atlas available in the Human Connectome Project (HCP)-1065 dataset (2017 Q4, 1,200-subject release) in DSI Studio. The deterministic tracking was performed with the manually selected regions of interest (ROIs) on this atlas according to prior anatomic knowledge. Templates were then applied to the MRI datasets of 30 health participants acquired from a single hospital to verify the practicability of the tracking. The diffusion tensor and shape analysis metrics were calculated for all LRCCP tracts. Differences in the tracking metrics between the left and right hemispheres were compared, and the related white matter asymmetry was discussed.

Results

The LRCCP templates were successfully created and applied to healthy participants for quantitative analysis. Significantly higher mean fractional anisotropy (FA) values were discovered on the left (L) corticorubral tract [L, 0.43±0.02 vs. right (R), 0.41±0.02; P<0.01] and left dentatorubrothalamic tract (L, 0.47±0.02 vs. R, 0.46±0.02; P<0.01). Significant differences in tract volume and streamline number were observed between the corticopontine, corticorubral, and dentatorubrothalamic tracts. The size of the right corticopontine and corticorubral tracts were smaller, and both had smaller streamline numbers and innervation areas when compared with the contralateral sides. The R dentatorubrothalamic tract showed a larger volume (R, 23,582.47±4,160.71 mm³ vs. L, 19,821.27±2,983.91 mm³; P<0.01) and innervation area (R, 2,117.37±433.98 mm² vs. L, 1,610.00±356.19 mm²; P<0.01) than did the L side. No significant differences were observed in the rubroolivary tracts.

Conclusions

This work suggests the feasibility of applying tractography templates of the LRCCP to quantitatively evaluate white matter properties associated with language function. Lateralized diffusion metrics were observed in preliminary experiments. LRCCP tractography-based research may provide a potential quantitative method to better understanding neuroplasticity.

Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies

PREMISE

The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables high-throughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification.

METHODS AND RESULTS

MuLES uses contrasting pixel color values to distinguish between leaf objects and their background area, eliminating the need for color threshold-based methods or color correction cards typically required in other software methods. The leaf morphometric parameters measured by this software, especially leaf aspect ratio, were able to distinguish between large populations of different accessions for the same species in a high-throughput manner.

CONCLUSIONS

MuLES provides a simple method for the rapid measurement of leaf morphometric parameters in large plant populations from digital images and demonstrates the ability of leaf aspect ratio to distinguish between closely related plant types.

Examination of Shape Variation of the Skull in British Shorthair, Scottish Fold, and Van Cats

A variety of skull shapes are frequently used for discrimination between animal species, breeds, and sexes. In this study, skulls of three different breeds of cats were examined by the geometric morphometric method, with the aim of revealing skull shape differences. For this purpose, 27 cats (6 British Shorthair, 7 Scottish Fold, and 14 Van cats) were used. The skulls of cats were modeled by computed tomography. Geometric morphometrics was applied using dorsal (8 landmarks, 63 semilandmarks) and lateral (8 landmarks, 63 semilandmarks) skull projections on these models. Centroid size differences between the breeds were statistically insignificant. However, the differences in shape were statistically significant for both the dorsal view and lateral view. Shape variation was less in the British Shorthair than in other breeds. Shape differences generally occurred around the orbit. In the skull of Scottish Folds, the orbit was situated more caudally than in other breeds. The British Shorthair had the largest orbital ring. In dorsal view, the Scottish Fold had the largest orbital diameter. The orbital ring of Van cats was smallest in both dorsal and lateral views. In the canonical variate analysis, it was seen that the breeds were separated from each other. The shape difference in the skull between different cat breeds could be revealed by geometric morphometrics. The results of this study provide useful information for taxonomy.

GC-MLP: Graph Convolution MLP for Point Cloud Analysis

With the objective of addressing the problem of the fixed convolutional kernel of a standard convolution neural network and the isotropy of features making 3D point cloud data ineffective in feature learning, this paper proposes a point cloud processing method based on graph convolution multilayer perceptron, named GC-MLP. Unlike traditional local aggregation operations, the algorithm generates an adaptive kernel through the dynamic learning features of points, so that it can dynamically adapt to the structure of the object, i.e., the algorithm first adaptively assigns different weights to adjacent points according to the different relationships between the different points captured. Furthermore, local information interaction is then performed with the convolutional layers through a weight-sharing multilayer perceptron. Experimental results show that, under different task benchmark datasets (including ModelNet40 dataset, ShapeNet Part dataset, S3DIS dataset), our proposed algorithm achieves state-of-the-art for both point cloud classification and segmentation tasks.

Using Optimal Transport to Improve Spherical Harmonic Quantification of Complex Biological Shapes

The knowledge of the anatomical shape of both gross and microscopic structures is the key to understanding the effects of disease processes on cellular structure. Geometric morphometric methods, such as Procrustes superimposition, and Spherical Harmonics (SPHARM), have been used to capture the biological shape variation and group differences in morphology. Previous SPHARM-MAT techniques use the CALD algorithm to parameterize the mesh surface. It starts from initial mapping and performs local and global smoothing methods alternately to control the area and length distortions simultaneously. However, this parameterization may not be sufficient in complex morphological cases. To bridge this gap, we propose SPHARM-OT, an enhanced SPHARM surface modeling method using optimal transport (OT) for spherical parameterization. First, the genus 0 3D objects are conformally mapped onto a sphere. Then the optimal transport theory via spherical power diagram is introduced to minimize the area distortion. This new algorithm can effectively reduce the area distortion and lead to a better reconstruction result. We demonstrate the effectiveness of the method by applying it to the human sphenoidal paranasal sinuses.

Comprehensive personalized ankle joint shape analysis of children with cerebral palsy from pediatric MRI

Cerebral palsy, a common physical disability in childhood, often causes abnormal patterns of movement and posture. To better understand the pathology and improve rehabilitation of patients, a comprehensive bone shape analysis approach is proposed in this article. First, a group analysis is performed on a clinical MRI dataset using two state-of-the-art shape analysis methods: ShapeWorks and a voxel-based method relying on Advanced Normalization Tools (ANTs) registration. Second, an analysis of three bones of the ankle is done to provide a complete view of the ankle joint. Third, a bone shape analysis is carried out at subject level to highlight variability patterns for personnalized understanding of deformities.

Classifying organisms and artefacts by their outline shapes

We often wish to classify objects by their shapes. Indeed, the study of shapes is an important part of many scientific fields, such as evolutionary biology, structural biology, image processing and archaeology. However, mathematical shape spaces are rather complicated and nonlinear. The most widely used methods of shape analysis, geometric morphometrics, treat the shapes as sets of points. Diffeomorphic methods consider the underlying curve rather than points, but have rarely been applied to real-world problems. Using a machine classifier, we tested the ability of several of these methods to describe and classify the shapes of a variety of organic and man-made objects. We find that one method, based on square-root velocity functions (SRVFs), outperforms all others, including a standard geometric morphometric method (eigenshapes), and that it is also superior to human experts using shape alone. When the SRVF approach is constrained to take account of homologous landmarks it can accurately classify objects of very different shapes. The SRVF method identifies a shortest path between shapes, and we show that this can be used to estimate the shapes of intermediate steps in evolutionary series. Diffeomorphic shape analysis methods, we conclude, now provide practical and effective solutions to many shape description and classification problems in the natural and human sciences.

Geometric analysis of otoliths in Cyprinion kais and Cyprinion macrostomus

Cyprinion macrostomus and Cyprinion kais are species that inhabit in the Tigris River. These fishes, formerly considered as the same species, have been listed as different species by taking differences in jaw and mouth structures into consideration. The mouth shape of C. kais is distinct and small. The mouth is convex and has broad lateral lobes. The mouth of C. macrostomus is wider, is convex and lacks lateral lobes. This study aimed to determine the shape-dependent variability in the breed and sex factors of otoliths of the fish species C. kais and C. macrostomus. For this purpose, 30 right otoliths from both species were used. Geometric morphometric analyses were performed by marking semilandmarks on the otoliths. When examining the results of the analysis, it was found that the first base component accounted for the total shape difference by 26.871% and the first three base components accounted for the total shape difference by 52.235%. In the regression analysis of shape on dimension, it was found that 2.1020% of shape could be estimated in terms of size according to the groups. In the wire-frame wrap graph showing group-based shape differences, it was found that C. kais was wider than C. macrostomus at the level of the dorsal margin and the rostrum region of C. macrostomus was larger and sharply pointed. Consequently, it is believed that the data of the study can be reference for many disciplines, especially for taxonomic classification of species.

Atrophy of the hippocampal CA1 subfield relates to long-term forgetting in focal epilepsy

OBJECTIVE

The mechanisms underlying accelerated long-term forgetting (ALF) in patients with epilepsy are still under investigation. We examined the contribution of hippocampal subfields and their morphology to long-term memory performance in patients with focal epilepsy.

METHODS

We prospectively assessed long-term memory and performed magnetic resonance imaging in 80 patients with focal epilepsy (61 with temporal lobe epilepsy and 19 with extratemporal lobe epilepsy) and 30 healthy controls. The patients also underwent electroencephalography recording. Verbal and visuospatial memory was tested 30 seconds, 10 minutes, and 1 week after learning. We assessed the volumes of the whole hippocampus and seven subfields and deformation of the hippocampal shape. The contributions of the hippocampal volumes and shape deformation to long-term forgetting, controlling for confounding factors, including the presence of interictal epileptiform discharges, were assessed by multiple regression analyses.

RESULTS

Patients with focal epilepsy had lower intelligence quotients and route recall scores at 10 minutes than controls. The focal epilepsy group had smaller volumes of both the right and left hippocampal tails than the control group, but there were no significant group differences for the volumes of the whole hippocampus or other hippocampal subfields. Multiple regression analyses showed a significant association between the left CA1 volume and the 1-week story retention (β = 7.76; Bonferroni-corrected P = 0.044), but this was not found for the whole hippocampus or other subfield volumes. Hippocampal shape analyses revealed that atrophy of the superior-lateral, superior-central, and inferior-medial regions of the left hippocampus, corresponding to CA1 and CA2/3, was associated with the verbal retention rate.

SIGNIFICANCE

Our results suggest that atrophy of the hippocampal CA1 region and its associated structures disrupts long-term memory consolidation in focal epilepsy. Neuronal cell loss in specific hippocampal subfields could be a key underlying cause of ALF in patients with epilepsy.

T cell morphodynamics reveal periodic shape oscillations in three-dimensional migration

T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralize infected and cancerous cells. However, there is limited quantitative understanding of the migration process in three-dimensional extracellular matrices (ECMs) and across timescales. Here, we leveraged recent advances in lattice light-sheet microscopy to quantitatively explore the three-dimensional morphodynamics of migrating T cells at high spatio-temporal resolution. We first developed a new shape descriptor based on spherical harmonics, incorporating key polarization information of the uropod. We found that the shape space of T cells is low-dimensional. At the behavioural level, run-and-stop migration modes emerge at approximately 150 s, and we mapped the morphodynamic composition of each mode using multiscale wavelet analysis, finding 'stereotyped' motifs. Focusing on the run mode, we found morphodynamics oscillating periodically (every approx. 100 s) that can be broken down into a biphasic process: front-widening with retraction of the uropod, followed by a rearward surface motion and forward extension, where intercalation with the ECM in both of these steps likely facilitates forward motion. Further application of these methods may enable the comparison of T cell migration across different conditions (e.g. differentiation, activation, tissues and drug treatments) and improve the precision of immunotherapeutic development.

Shapes of subcortical structures in adolescents with and without familial history of substance use disorder

It has been suggested that intergenerational transmission of risk for substance use disorder (SUD) manifests in the brain anatomy of substance naïve adolescents. While volume and shapes of subcortical structures (SSS) have been shown to be heritable, these structures, especially the pallidum, putamen, nucleus accumbens, and hippocampus, have also been associated with substance use disorders. However, it is not clear if those anatomical differences precede substance use or are the result of that use. Therefore, we examined if volume and SSS of adolescents with a family history (FH+) of SUD differed from adolescents without such a history (FH−). Because risk for SUD is associated with anxiety and impulsivity, we also examined correlations between these psychological characteristics and volume/SSS. Using structural MRI and FSL software, we segmented subcortical structures and obtained indices of SSS and volumes of 64 FH+ and 58 FH− adolescents. We examined group differences in volume and SSS, and the correlations between volume/SSS and trait anxiety and impulsivity. FH+ adolescents had a significant inward deformation in the shape of the right anterior hippocampus compared to FH− adolescents, while the volume of this structure did not differ between groups. Neither shape nor volume of the other subcortical structures differed between groups. In the FH+ adolescents, the left hippocampus shape was positively correlated with both trait anxiety and impulsivity, while in FH− adolescents a negative correlation pattern of SSS was seen in the hippocampus. SSS appears to capture local anatomical features that traditional volumetric analysis does not. The inward shape deformation in the right anterior hippocampus in FH+ adolescents may be related to the known increased risk for behavioral dysregulation leading to SUD in FH+ offspring. Hippocampus shape also exhibits opposite patterns of correlation with anxiety and impulsivity scores across the FH+ and FH− adolescents. These novel findings may reveal neural correlates, not captured by traditional volumetric analysis, of familial transmission of increased vulnerability to SUD.

Cortical and Subcortical Structural Abnormalities in Patients With Idiopathic Cervical and Generalized Dystonia

OBJECTIVES

In this study, we sought to investigate structural imaging alterations of patients with idiopathic dystonia at the cortical and subcortical levels. The common and specific changes in two subtypes of dystonia, cervical dystonia (CD) and generalized dystonia (GD), were intended to be explored. Additionally, we sought to identify the morphometric measurements which might be related to patients' clinical characteristics, thus providing more clues of specific brain regions involved in the mechanism of idiopathic dystonia.

METHODS

3D T1-weighted MRI scans were acquired from 56 patients with idiopathic dystonia and 30 healthy controls (HC). Patients were classified as CD or GD, according to the distinct symptom distributions. Cortical thickness (CT) of 30 CD and 26 GD were estimated and compared to HCs using Computational Anatomy Toolbox (CAT12), while volumes of subcortical structures and their shape alterations (29 CD, 25 GD, and 27 HCs) were analyzed via FSL software. Further, we applied correlation analyses between the above imaging measurements with significant differences and patients' clinical characteristics.

RESULTS

The results of comparisons between the two patient groups and HCs were highly consistent, demonstrating increased CT of bilateral postcentral, superiorparietal, superiorfrontal/rostralmiddlefrontal, occipital gyrus, etc., and decreased CT of bilateral cingulate, insula, entorhinal, and fusiform gyrus (PFWE < 0.005 at the cluster level). In CD, trends of negative correlations were found between disease severity and CT alterations mostly located in pre/postcentral, rostralmiddlefrontal, superiorparietal, and supramarginal regions. Besides, volumes of bilateral putamen, caudate, and thalamus were significantly reduced in both patient groups, while pallidum volume reduction was also presented in GD compared to HCs. Caudate volume reduction had a trend of correlation to increasing disease severity in GD. Last, shape analysis directly demonstrated regional surface alterations in bilateral thalamus and caudate, where the atrophy located in the head of caudate had a trend of correlation to earlier ages of onset in GD.

CONCLUSIONS

Our study demonstrates wide-spread morphometric changes of CT, subcortical volumes, and shapes in idiopathic dystonia. CD and GD presented similar patterns of morphometric abnormalities, indicating shared underlying mechanisms in two different disease forms. Especially, the clinical associations of CT of multiple brain regions with disease severity, and altered volume/shape of caudate with disease severity/age of onset separately in CD and GD might serve as potential biomarkers for further disease exploration.

Variations in Dietary Patterns Defined by the Healthy Eating Index 2015 and Associations with Mortality: Findings from the Dietary Patterns Methods Project

BACKGROUND

It is currently unknown if within high-quality dietary intake there exist distinct dietary patterns associated with health benefits that are identifiable with multidimensional dietary pattern analyses. The purpose of this study was to identify specific dietary patterns and groups therein and their associations with all-cause, CVD, and cancer mortality.

METHODS

We conducted sex-specific k-means cluster analyses within Healthy Eating Index 2015 (HEI-2015) quintile 5 in 3 US cohorts [NIH-American Association of Retired Persons Diet and Health Study (AARP), the Multiethnic Cohort (MEC), Women's Health Initiative Observational Study (WHI OS)], clusters ranging from n = 1190 to n = 12,007. Characterizations incorporated HEI-2015 overall and component-specific percentage adherence goals, using untruncated and truncated radar graphs and shape analyses. Using cohort- and sex-specific Cox proportional hazards models, associations of quintile 5 clusters with all-cause, cardiovascular disease (CVD), and cancer mortality were evaluated relative to quintile 1.

RESULTS

In each cohort sex-specific sample, 3 identified clusters included 16%-62% of participants, providing evidence for variation within high-quality dietary intake. Clusters revealed commonalities in total fruits and whole fruits intakes that exceeded goals and high sodium intake. Dairy and whole grain intakes oftentimes fell below goal. Some clusters were in addition characterized by total vegetables, greens & beans, and seafood & plant protein intakes exceeding goals. All high-quality dietary patterns were associated with a multivariable-adjusted significant 15%-26% lower risk of all-cause death than diet intake in quintile 1 (except for cluster 2 in WHI OS), and with a 16%-25% lower risk of CVD mortality in the AARP and MEC cohorts. Cancer mortality results were inconsistent.

CONCLUSIONS

Multiple ways to achieve a high-quality diet were identified and significant associations with lower all-cause and CVD mortality were seen in some cohorts.

A new framework for analysis of three-dimensional shape and architecture of human skeletal muscles from in vivo imaging data

A new framework is presented for comprehensive analysis of the three-dimensional shape and architecture of human skeletal muscles from magnetic resonance and diffusion tensor imaging data. The framework comprises three key features: (1) identification of points on the surface of and inside a muscle that have a correspondence to points on and inside another muscle, (2) reconstruction of average muscle shape and average muscle fibre orientations, and (3) utilization of data on between-muscle variation to visualize and make statistical inferences about changes or differences in muscle shape and architecture. The general use of the framework is demonstrated by its application to three case studies. Analysis of data obtained before and after eight weeks of strength training revealed there was little regional variation in hypertrophy of the vastus medialis and vastus lateralis, and no systematic change in pennation angle. Analysis of passive muscle lengthening revealed heterogeneous changes in shape of the medial gastrocnemius, and confirmed the ability of the methods to detect subtle changes in muscle fibre orientation. Analysis of the medial gastrocnemius of children with unilateral cerebral palsy showed that muscles in the more-affected limb were shorter, thinner and less wide than muscles in the less-affected limb, and had slightly more pennate muscle fibres in the central and proximal part of the muscle. Amongst other applications, the framework can be used to explore the mechanics of muscle contraction, investigate adaptations of muscle architecture, build anatomically realistic computational models of skeletal muscles, and compare muscle shape and architecture between species.

Changes in the Shape and Volume of Subcortical Structures in Patients With End-Stage Renal Disease

Introduction: End-stage renal disease (ESRD) typically causes changes in brain structure, and patients with ESRD often experience cognitive and sleep disorders. We aimed to assess the changes in the subcortical structure of patients with ESRD and how they are associated with cognitive and sleep disorders.

Methods: We involved 36 adult patients for maintenance hemodialysis and 35 age- and gender-matched control individuals. All participants underwent neuropsychological examination and 3T magnetic resonance imaging (MRI) to acquire T1 anatomical images. The laboratory blood tests were performed in all patients with ESRD close to the time of the MR examination. We used volumetric and vertex-wise shape analysis approaches to investigate the volumes of 14 subcortical structural (e.g., bilateral accumbens, amygdala, hippocampus, caudate, globus pallidus, putamen, and thalamus) abnormalities in the two groups. Analyses of partial correlations and shape correlations were performed in order to identify the associations between subcortical structure, cognition, and sleep quality in patients with ESRD.

Results: The volumetric analysis showed that compared with the healthy control group, patients with ESRD had less bilateral thalamus (left: p < 0.001; right: p < 0.001), bilateral accumbens (left: p < 0.001; right: p = 0.001), and right amygdala (p = 0.002) volumes. In the vertex-wise shape analysis, patients with ESRD had abnormal regional surface atrophy in the bilateral thalamus, right accumbens, left putamen, and bilateral caudate. Moreover, the Montreal Cognitive Assessment (MoCA) score was associated with volume reduction in the bilateral thalamus (left: Spearman ρ = 0.427, p = 0.009; right: ρ = 0.319, p = 0.018), and the Pittsburgh Sleep Quality Index (PSQI) score was associated with volume reduction in the bilateral accumbens (left: ρ = −0.546, p = 0.001; right: ρ = −0.544, p = 0.001). In vertex-wise shape correlation analysis, there was a positive significant correlation between regional shape deformations on the bilateral thalamus and MoCA score in patients with ESRD.

Conclusion: Our study suggested that patients with ESRD have subcortical structural atrophy, which is related to impaired cognitive performance and sleep disturbances. These findings may help to further understand the underlying neural mechanisms of brain changes in patients with ESRD.

Mechanistic Modeling of Longitudinal Shape Changes: Equations of Motion and Inverse Problems

This paper examines a longitudinal shape evolution model in which a three-dimensional volume progresses through a family of elastic equilibria in response to the time-derivative of an internal force, or yank, with an additional regularization to ensure diffeomorphic transformations. We consider two different models of yank and address the long time existence and uniqueness of solutions for the equations of motion in both models. In addition, we derive sufficient conditions for the existence of an optimal yank that best describes the change from an observed initial volume to an observed volume at a later time. The main motivation for this work is the understanding of processes such as growth and atrophy in anatomical structures, where the yank could be roughly interpreted as a metabolic event triggering morphological changes. We provide preliminary results on simple examples to illustrate, under this model, the retrievability of some attributes of such events.

Parallel tempering strategies for model-based landmark detection on shapes

In the field of shape analysis, landmarks are defined as a low-dimensional, representative set of important features of an object's shape that can be used to identify regions of interest along its outline. An important problem is to infer the number and arrangement of landmarks, given a set of shapes drawn from a population. One proposed approach defines a posterior distribution over landmark locations by associating each landmark configuration with a linear reconstruction of the shape. In practice, sampling from the resulting posterior density is challenging using standard Markov chain Monte Carlo (MCMC) methods because multiple configurations of landmarks can describe a complex shape similarly well, manifesting in a multi-modal posterior with well-separated modes. Standard MCMC methods traverse multi-modal posteriors poorly and, even when multiple modes are identified, the relative amount of time spent in each one can be misleading. We apply new advances in the parallel tempering literature to the problem of landmark detection, providing guidance on implementation generalized to other applications within shape analysis. Proposal adaptation is used during burn-in to ensure efficient traversal of the parameter space while maintaining computational efficiency. We demonstrate this algorithm on simulated data and common shapes obtained from computer vision scenes.

Heterogeneity of PD-MCI in Candidates to Subthalamic Deep Brain Stimulation: Associated Cortical and Subcortical Modifications

BACKGROUND

Parkinson's disease mild cognitive impairment (PD-MCI) is frequent and heterogenous. There is no consensus about its influence on subthalamic deep brain stimulation (STN-DBS) outcomes.

OBJECTIVE

To determine the prevalence of PD-MCI and its subtypes in candidates to STN-DBS. Secondarily, we sought to identify MRI structural markers associated with cognitive impairment in these subgroups.

METHODS

Baseline data from the French multicentric PREDISTIM cohort were used. Candidates to STN-DBS were classified according to their cognitive performance in normal cognition (PD-NC) or PD-MCI. The latter included frontostriatal (PD-FS) and posterior cortical (PD-PC) subtypes. Between-group comparisons were performed on demographical and clinical variables as well as on T1-weighted MRI sequences at the cortical and subcortical levels.

RESULTS

320 patients were included: 167 (52%) PD-NC and 153 (48%) PD-MCI patients. The latter group included 123 (80%) PD-FS and 30 (20%) PD-PC patients. There was no between-group difference regarding demographic and clinical variables. PD-PC patients had significantly lower global efficiency than PD-FS patients and significantly worse performance on visuospatial functions, episodic memory, and language. Compared to PD-NC, PD-MCI patients had cortical thinning and radiomic-based changes in the left caudate nucleus and hippocampus. There were no significant differences between the PD-MCI subtypes.

CONCLUSION

Among the candidates to STN-DBS, a significant proportion has PD-MCI which is associated with cortical and subcortical alterations. Some PD-MCI patients have posterior cortical deficits, a subtype known to be at higher risk of dementia.

Hippocampal Asymmetry of Regional Development and Structural Covariance in Preterm Neonates

Premature birth is associated with a high prevalence of neurodevelopmental impairments in surviving infants. The hippocampus is known to be critical for learning and memory, yet the putative effects of hippocampal dysfunction remain poorly understood in preterm neonates. In particular, while asymmetry of the hippocampus has been well noted both structurally and functionally, how preterm birth impairs hippocampal development and to what extent the hippocampus is asymmetrically impaired by preterm birth have not been well delineated. In this study, we compared volumetric growth and shape development in the hippocampal hemispheres and structural covariance (SC) between hippocampal vertices and cortical thickness in cerebral cortex regions between two groups. We found that premature infants had smaller volumes of the right hippocampi only. Lower thickness was observed in the hippocampal head in both hemispheres for preterm neonates compared with full-term peers, though preterm neonates exhibited an accelerated age-related change of hippocampal thickness in the left hippocampi. The SC between the left hippocampi and the limbic lobe of the premature infants was severely impaired compared with the term-born neonates. These findings suggested that the development of the hippocampus during the third trimester may be altered following early extrauterine exposure with a high degree of asymmetry.

Morphometry Difference of the Hippocampal Formation Between Blind and Sighted Individuals

The detailed morphometry alterations of the human hippocampal formation (HF) for blind individuals are still understudied. 50 subjects were recruited from Yantai Affiliated Hospital of Binzhou Medical University, including 16 congenital blindness, 14 late blindness, and 20 sighted controls. Volume and shape analysis were conducted between the blind (congenital or late) and sighted groups to observe the (sub)regional alterations of the HF. No significant difference of the hippocampal volume was observed between the blind and sighted subjects. Rightward asymmetry of the hippocampal volume was found for both congenital and late blind individuals, while no significant hemispheric difference was observed for the sighted controls. Shape analysis showed that the superior and inferior parts of both the hippocampal head and tail expanded, while the medial and lateral parts constrained for the blind individuals as compared to the sighted controls. The morphometry alterations for the congenital blind and late blind individuals are nearly the same. Significant expansion of the superior part of the hippocampal tail for both congenital and late blind groups were observed for the left hippocampi after FDR correction. Current results suggest that the cross-model plastic may occur in both hemispheres of the HF to improve the navigation ability without the stimuli of visual cues, and the alteration is more prominent for the left hemisphere.

Hippocampal subregional alterations and verbal fluency in the early stage of type 2 diabetes mellitus

Growing evidence indicates that type 2 diabetes mellitus (T2DM)-related cognitive dysfunction may develop in the early stage of the disease and is often accompanied by hippocampal structural alterations. In the current study, we investigated volume and shape alterations of the hippocampus at a subregional level in patients with T2DM. With the use of high-resolution brain structural images that were obtained from 30 T2DM patients with less than 5 years of disease duration and 30 healthy individuals, volumetric and shape analyses were performed. We also assessed the relationship between T2DM-related hippocampal structural alterations and performance on verbal fluency. In volumetric analysis, total hippocampal volume was smaller in the T2DM group, relative to the control group. At a subregional level, T2DM patients showed significant inward deformation and volume reduction of the right dentate gyrus and cornu ammonis 2/3 subregions as compared with healthy individuals. In particular, T2DM patients with lower performance on verbal fluency had smaller right dentate gyrus volumes relative to those with higher performance. These findings suggest that the hippocampus may undergo atrophy at a subregional level even in the early stage of T2DM, and this subregion-specific atrophy may be associated with reduced performance on verbal fluency.

EVOLUTIONARY DE RHAM-HODGE METHOD

The de Rham-Hodge theory is a landmark of the 20^th Century's mathematics and has had a great impact on mathematics, physics, computer science, and engineering. This work introduces an evolutionary de Rham-Hodge method to provide a unified paradigm for the multiscale geometric and topological analysis of evolving manifolds constructed from a filtration, which induces a family of evolutionary de Rham complexes. While the present method can be easily applied to close manifolds, the emphasis is given to more challenging compact manifolds with 2-manifold boundaries, which require appropriate analysis and treatment of boundary conditions on differential forms to maintain proper topological properties. Three sets of unique evolutionary Hodge Laplacians are proposed to generate three sets of topology-preserving singular spectra, for which the multiplicities of zero eigenvalues correspond to exactly the persistent Betti numbers of dimensions 0, 1 and 2. Additionally, three sets of non-zero eigenvalues further reveal both topological persistence and geometric progression during the manifold evolution. Extensive numerical experiments are carried out via the discrete exterior calculus to demonstrate the potential of the proposed paradigm for data representation and shape analysis of both point cloud data and density maps. To demonstrate the utility of the proposed method, the application is considered to the protein B-factor predictions of a few challenging cases for which existing biophysical models break down.

Validation of Skully Care as a Fast Method for Quantifying Positional Cranial Deformities

Objective

Craniofacial measuring is valuable for diagnosis and evaluation of growth and treatment of positional skull deformities. Plagiocephalometry (PCM) quantifies skull deformities and is proven to be reliable and valid. However, PCM needs direct skin contact with thermoplastic material, is laborious and time-consuming. Therefore, Skully Care (SC) was developed to measure positional skull deformities with a smartphone application.

Design

SC is retrospectively compared to PCM.

Setting

Pediatric physiotherapy centers.

Patients

Age ≤1 year, analyzed or treated for positional skull deformities.

Interventions

A total of 60 skull shape analyses were performed.

Main Outcome Measures

The main outcome measures employed are Pearson correlation coefficient between cranial vault asymmetry index (CVAI; in SC) and oblique diameter difference index (ODDI; in PCM) and between cranial index (CI; in SC) and cranial proportional index (CPI; in PCM). Mann–Whitney U test determined difference of time consumption between PCM and SC.

Results

High correlation was found between CVAI and ODDI (r = 0.849; P < .01) in positional plagiocephaly and very high correlation between CI and CPI (r = 0.938; P < .01) in positional brachycephaly. SC is significantly faster than PCM (P < .001).

Conclusions

SC is valid in analyzing positional skull deformities and strongly correlates to PCM, the gold standard in daily physiotherapy practice. The combination of simplicity, validity, speed, and user and child convenience makes SC a promising craniofacial measuring method in daily practice. SC has potential to be the modern successor for analyzing positional skull deformities.

USING MULTIVARIATE ANALYSES TO EXPLORE DISEASE PROGRESSION OF FINCH MYCOPLASMOSIS

Lesion severity scales have been developed for a number of wildlife diseases causing external pathology. Perhaps the best known and most widely used scoring system has been developed for finch mycoplasmosis in which observers measure conjunctival pathology along a four-point scale of increasing severity. We developed novel techniques to characterize variation in host phenotype based on occupancy of multidimensional trait space (disease space). First, we used shape analysis to track distortions of the inner and outer eye rims, defined by 16 anatomical landmarks. Then, we used community analysis to evaluate pathology based on the presence or absence of a unique set of binary descriptors. We applied these techniques to experimental infection data to relate differences in conjunctival pathology to stage of infection. Specifically, by comparing specimens that received the same severity score at different time points in infection, we asked if shape or community analyses could distinguish between individuals in early infection versus those in recovery. We found that individual eyes followed predictable loops through disease space, tracking further from their origin with more severe pathology. Also, certain pathological descriptors were more likely to appear earlier versus later in infection. Our results indicated that leveraging differences in pathology captured in complex trait space could complement severity scores by better resolving the time course of infection from limited data points.

Morphological Analysis of the Right Ventricular Endocardial Wall in Pulmonary Hypertension

Pulmonary hypertension (PH) is a chronic progressive disease diagnosed when the pressure in the main pulmonary artery, assessed by right heart catheterization (RHC), is greater than 25 mmHg. Changes in the pulmonary vasculature due to the high pressure yield an increase in the right ventricle (RV) afterload. This starts a remodeling process during which the ventricle exhibits changes in shape and eventually fails. RV models were obtained from the segmentation of cardiac magnetic resonance images at baseline and 1-year follow-up for a pilot study that involved 12 PH and 7 control subjects. The models were used to create surface meshes of the geometry and to compute the principal, mean, and Gaussian curvatures. Ten global curvature indices were calculated for each of the RV endocardial wall reconstructions at the end-diastolic volume (EDV) and end-systolic volume (ESV) phases of the cardiac cycle. Statistical analysis of the data was performed to discern if there are significant differences in the curvature indices between controls and the PH group, as well as between the baseline and follow-up phases for the PH subjects. Six curvature indices, namely, the Gaussian curvature at ESV, the mean curvature at EDV and ESV, the L2-norm of the mean curvature at ESV, and the L2-norm of the major principal curvature at EDV and ESV, were found to be significantly different between controls and PH subjects (p < 0.05). We infer that these geometry measures could be used as indicators of RV endocardial wall morphology changes. Two global parameters, the Gaussian and mean curvatures at ESV, showed significant changes at the one-year follow-up for the PH subjects (p < 0.05). The aforementioned geometry measures to assess changes in RV shape could be used as part of a noninvasive computational tool to aid clinicians in PH diagnostic and progression assessment, and to evaluate the effectiveness of treatment.

Motor abnormalities and basal ganglia in first-episode psychosis (FEP)

BACKGROUND

Motor abnormalities (MAs) are the primary manifestations of schizophrenia. However, the extent to which MAs are related to alterations of subcortical structures remains understudied.

METHODS

We aimed to investigate the associations of MAs and basal ganglia abnormalities in first-episode psychosis (FEP) and healthy controls. Magnetic resonance imaging was performed on 48 right-handed FEP and 23 age-, gender-, handedness-, and educational attainment-matched controls, to obtain basal ganglia shape analysis, diffusion tensor imaging techniques (fractional anisotropy and mean diffusivity), and relaxometry (R2*) to estimate iron load. A comprehensive motor battery was applied including the assessment of parkinsonism, catatonic signs, and neurological soft signs (NSS). A fully automated model-based segmentation algorithm on 1.5T MRI anatomical images and accurate corregistration of diffusion and T2* volumes and R2* was used.

RESULTS

FEP patients showed significant local atrophic changes in left globus pallidus nucleus regarding controls. Hypertrophic changes in left-side caudate were associated with higher scores in sensory integration, and in right accumbens with tremor subscale. FEP patients showed lower fractional anisotropy measures than controls but no significant differences regarding mean diffusivity and iron load of basal ganglia. However, iron load in left basal ganglia and right accumbens correlated significantly with higher extrapyramidal and motor coordination signs in FEP patients.

CONCLUSIONS

Taken together, iron load in left basal ganglia may have a role in the emergence of extrapyramidal signs and NSS of FEP patients and in consequence in the pathophysiology of psychosis.

Brainstem Involvement in Amyotrophic Lateral Sclerosis: A Combined Structural and Diffusion Tensor MRI Analysis

Introduction

The brainstem is an important component in the pathology of amyotrophic lateral sclerosis (ALS). Although neuroimaging studies have shown multiple structural changes in ALS patients, few studies have investigated structural alterations in the brainstem. Herein, we compared the brainstem structure between patients with ALS and healthy controls.

Methods

A total of 33 patients with ALS and 33 healthy controls were recruited in this study. T1-weighted and diffusion tensor imaging (DTI) were acquired on a 3 Tesla magnetic resonance imaging (3T MRI) scanner. Volumetric and vertex-wised approaches were implemented to assess the differences in the brainstem’s morphological features between the two groups. An atlas-based region of interest (ROI) analysis was performed to compare the white matter integrity of the brainstem between the two groups. Additionally, a correlation analysis was used to evaluate the relationship between ALS clinical characteristics and structural features.

Results

Volumetric analyses showed no significant difference in the subregion volume of the brainstem between ALS patients and healthy controls. In the shape analyses, ALS patients had a local abnormal surface contraction in the ventral medulla oblongata and ventral pons. Compared with healthy controls, ALS patients showed significantly lower fractional anisotropy (FA) in the left corticospinal tract (CST) and bilateral frontopontine tracts (FPT) at the brainstem level, and higher radial diffusivity (RD) in bilateral CST and left FPT at the brainstem level by ROI analysis in DTI. Correlation analysis showed that disease severity was positively associated with FA in left CST and left FPT.

Conclusion

These findings suggest that the brainstem in ALS suffers atrophy, and degenerative processes in the brainstem may reflect disease severity in ALS. These findings may be helpful for further understanding of potential neural mechanisms in ALS.

A morphological trait involved in reproductive isolation between Drosophila sister species is sensitive to temperature

Male genitalia are usually extremely divergent between closely related species, but relatively constant within one species. Here we examine the effect of temperature on the shape of the ventral branches, a male genital structure involved in reproductive isolation, in the sister species Drosophila santomea and Drosophila yakuba. We designed a semi-automatic measurement machine learning pipeline that can reliably identify curvatures and landmarks based on manually digitized contours of the ventral branches. With this method, we observed that temperature does not affect ventral branches in D. yakuba but that in D. santomea ventral branches tend to morph into a D. yakuba-like shape at lower temperature. We found that male genitalia structures involved in reproductive isolation can be relatively variable within one species and can resemble the shape of closely related species' genitalia through plasticity to temperature. Our results suggest that reproductive isolation mechanisms can be dependent on the environmental context.

Shape Analysis as an Additional Tool in Roe Deer (Capreolus capreolus) Management: A New Approach Based on the Relationship between Mandible Shape and Trophic Resources

Simple Summary

In recent years, the numerical increase of the roe deer population in Italy has shifted attention to new tools for the management of these populations. The use of biometric data for a correct assessment of the status of ungulate populations is now a standardized and commonly used procedure. In this study, we tried to verify whether, in addition to biometric analyses, morphometrics could be used as a supplementary tool for roe deer management. The study of geometric morphometry has made a major impact by aiding technological and methodological advances. By using Cartesian coordinates of reference points, this method is capable of capturing morphologically distinct shape variables, which can be used as rapid indicators of the status of populations, and thus have the potential to be very useful for wildlife management.

Abstract

The analysis of body shape variability has always been a central element in biology. More recently, geometric morphometry has developed as a new field in shape analysis, with the aim to study body morphological variations and the identification of their causes. In wildlife management, geometric morphometry could be a useful tool to compare the anatomical structures of an organism and quantify its geometric information in order to relate them to environmental factors, thus identifying the causes and effects of the variation and acting management and/or conservation plans. The aim of our study is to evaluate the relationship between roe deer mandible shape and trophic resources available during autumn and winter. We applied a geometric morphometry approach consisting of a Relative Warp analysis of landmark data in 26 roe deer fawn mandibles. Each sample was assigned to an age category and to an environmental category based on the territory carrying capacity. The mandible shape of samples under 8 months of age is likely influenced by the availability of trophic resources. Our findings suggest that the mandible shape is a reliable instrument to assess resource availability. Geometric morphometry could thus represent an additional tool for roe deer management.

Posterior Cortical Cognitive Deficits Are Associated With Structural Brain Alterations in Mild Cognitive Impairment in Parkinson's Disease

Context: Cognitive impairments are common in patients with Parkinson's disease (PD) and are heterogeneous in their presentation. The "dual syndrome hypothesis" suggests the existence of two distinct subtypes of mild cognitive impairment (MCI) in PD: a frontostriatal subtype with predominant attentional and/or executive deficits and a posterior cortical subtype with predominant visuospatial, memory, and/or language deficits. The latter subtype has been associated with a higher risk of developing dementia. Objective: The objective of this study was to identify structural modifications in cortical and subcortical regions associated with each PD-MCI subtype. Methods: One-hundred and fourteen non-demented PD patients underwent a comprehensive neuropsychological assessment as well as a 3T magnetic resonance imaging scan. Patients were categorized as having no cognitive impairment (n = 41) or as having a frontostriatal (n = 16), posterior cortical (n = 25), or a mixed (n = 32) MCI subtype. Cortical regions were analyzed using a surface-based Cortical thickness (CTh) method. In addition, the volumes, shapes, and textures of the caudate nuclei, hippocampi, and thalami were studied. Tractometric analyses were performed on associative and commissural white matter (WM) tracts. Results: There were no between-group differences in volumetric measurements and cortical thickness. Shape analyses revealed more abundant and more extensive deformations fields in the caudate nuclei, hippocampi, and thalami in patients with posterior cortical deficits compared to patients with no cognitive impairment. Decreased fractional anisotropy (FA) and increased mean diffusivity (MD) were also observed in the superior longitudinal fascicle, the inferior fronto-occipital fascicle, the striato-parietal tract, and the anterior and posterior commissural tracts. Texture analyses showed a significant difference in the right hippocampus of patients with a mixed MCI subtype. Conclusion: PD-MCI patients with posterior cortical deficits have more abundant and more extensive structural alterations independently of age, disease duration, and severity, which may explain why they have an increased risk of dementia.

Toward a Three-Dimensional Chromosome Shape Alphabet

The study of the three-dimensional (3D) structure of chromosomes-the largest macromolecules in biology-is one of the most challenging to date in structural biology. Here, we develop a novel representation of 3D chromosome structures, as sequences of shape letters from a finite shape alphabet, which provides a compact and efficient way to analyze ensembles of chromosome shape data, akin to the analysis of texts in a language by using letters. We construct a Chromosome Shape Alphabet from an ensemble of chromosome 3D structures inferred from Hi-C data-via SIMBA3D or other methods-by segmenting curves based on topologically associating domains (TADs) boundaries, and by clustering all TADs' 3D structures into groups of similar shapes. The median shapes of these groups, with some pruning and processing, form the Chromosome Shape Letters (CSLs) of the alphabet. We provide a proof of concept for these CSLs by reconstructing independent test curves by using only CSLs (and corresponding transformations) and comparing these reconstructions with the original curves. Finally, we demonstrate how CSLs can be used to summarize shapes in an ensemble of chromosome 3D structures by using generalized sequence logos.

Hippocampal and Amygdalar Morphological Abnormalities in Alzheimer's Disease Based on Three Chinese MRI Datasets

BACKGROUND

Early detection of Alzheimer's disease (AD) and its early stage, the mild cognitive impairment (MCI), has important scientific, clinical and social significance. Magnetic resonance imaging (MRI) based statistical shape analysis provides an opportunity to detect regional structural abnormalities of brain structures caused by AD and MCI.

OBJECTIVE

In this work, we aimed to employ a well-established statistical shape analysis pipeline, in the framework of large deformation diffeomorphic metric mapping, to identify and quantify the regional shape abnormalities of the bilateral hippocampus and amygdala at different prodromal stages of AD, using three Chinese MRI datasets collected from different domestic hospitals.

METHODS

We analyzed the region-specific shape abnormalities at different stages of the neuropathology of AD by comparing the localized shape characteristics of the bilateral hippocampi and amygdalas between healthy controls and two disease groups (MCI and AD). In addition to group comparison analyses, we also investigated the association between the shape characteristics and the Mini Mental State Examination (MMSE) of each structure of interest in the disease group (MCI and AD combined) as well as the discriminative power of different morphometric biomarkers.

RESULTS

We found the strongest disease pathology (regional atrophy) at the subiculum and CA1 subregions of the hippocampus and the basolateral, basomedial as well as centromedial subregions of the amygdala. Furthermore, the shape characteristics of the hippocampal and amygdalar subregions exhibiting the strongest AD related atrophy were found to have the most significant positive associations with the MMSE. Employing the shape deformation marker of the hippocampus or the amygdala for automated MCI or AD detection yielded a significant accuracy boost over the corresponding volume measurement.

CONCLUSION

Our results suggested that the amygdalar and hippocampal morphometrics, especially those of shape morphometrics, can be used as auxiliary indicators for monitoring the disease status of an AD patient.

FlyBy CNN: A 3D surface segmentation framework

In this paper, we present FlyBy CNN, a novel deep learning based approach for 3D shape segmentation. FlyByCNN consists of sampling the surface of the 3D object from different view points and extracting surface features such as the normal vectors. The generated 2D images are then analyzed via 2D convolutional neural networks such as RUNETs. We test our framework in a dental application for segmentation of intra-oral surfaces. The RUNET is trained for the segmentation task using image pairs of surface features and image labels as ground truth. The resulting labels from each segmented image are put back into the surface thanks to our sampling approach that generates 1-1 correspondence of image pixels and triangles in the surface model. The segmentation task achieved an accuracy of 0.9.

A Deformation-Based Shape Study of the Corpus Callosum in First Episode Schizophrenia

Background: Previous first-episode schizophrenia (FES) studies have reported abnormalities in the volume and mid-sagittal size of the corpus callosum (CC), but findings have been inconsistent. Besides, the CC shape has rarely been analyzed in FES. Therefore, in this study, we investigated FES-related CC shape abnormalities using 198 participants [92 FES patients and 106 healthy controls (HCs)]. Methods: We conducted statistical shape analysis of the mid-sagittal CC curve in a large deformation diffeomorphic metric mapping framework. The CC was divided into the genu, body, and splenium (gCC, bCC, and sCC) to target the key CC sub-regions affected by the FES pathology. Gender effects have been investigated. Results: There were significant area differences between FES and HC in the entire CC and gCC but not in bCC nor sCC. In terms of the localized shape morphometrics, significant region-specific shape inward-deformations were detected in the superior portion of gCC and the anterosuperior portion of bCC in FES. These global area and local shape morphometric abnormalities were restricted to female FES but not male FES. Conclusions: gCC was significantly affected in the neuropathology of FES and this finding was specific to female FES. This study suggests that gCC may be a key sub-region that is vulnerable to the neuropathology of FES, specifically in female patients. The morphometrics of gCC may serve as novel and efficient biomarkers for screening female FES patients.

A 7 Tesla Amygdalar-Hippocampal Shape Analysis of Lithium Response in Bipolar Disorder

Research to discover clinically useful predictors of lithium response in patients with bipolar disorder has largely found them to be elusive. We demonstrate here that detailed neuroimaging may have the potential to fill this important gap in mood disorder therapeutics. Lithium treatment and bipolar disorder have both been shown to affect anatomy of the hippocampi and amygdalae but there is no consensus on the nature of their effects. We aimed to investigate structural surface anatomy changes in amygdala and hippocampus correlated with treatment response in bipolar disorder. Patients with bipolar disorder (N = 14) underwent lithium treatment, were classified by response status at acute and long-term time points, and scanned with 7 Tesla structural MRI. Large Deformation Diffeomorphic Metric Mapping was applied to detect local differences in hippocampal and amygdalar anatomy between lithium responders and non-responders. Anatomy was also compared to 21 healthy comparison participants. A patch of the ventral surface of the left hippocampus was found to be significantly atrophied in non-responders as compared to responders at the acute time point and was associated at a trend-level with long-term response status. We did not detect an association between response status and surface anatomy of the right hippocampus or amygdala. To the best of our knowledge, this is the first shape analysis of hippocampus and amygdala in bipolar disorder using 7 Tesla MRI. These results can inform future work investigating possible neuroimaging predictors of lithium response in bipolar disorder.