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.