The effect of root hairs on root water uptake is determined by root-soil contact and root hair shrinkage

The effect of root hairs on water uptake remains controversial. In particular, the key root hair and soil parameters that determine their importance have been elusive. We grew maize plants (Zea mays) in microcosms and scanned them using synchrotron-based X-ray computed microtomography. By means of image-based modelling, we investigated the parameters determining the effectiveness of root hairs in root water uptake. We explicitly accounted for rhizosphere features (e.g. root-soil contact and pore structure) and took root hair shrinkage of dehydrated root hairs into consideration. Our model suggests that > 85% of the variance in root water uptake is explained by the hair-induced increase in root-soil contact. In dry soil conditions, root hair shrinkage reduces the impact of hairs substantially. We conclude that the effectiveness of root hairs on root water uptake is determined by the hair-induced increase in root-soil contact and root hair shrinkage. Although the latter clearly reduces the effect of hairs on water uptake, our model still indicated facilitation of water uptake by root hairs at soil matric potentials from -1 to -0.1 MPa. Our findings provide new avenues towards a mechanistic understanding of the role of root hairs on water uptake.

Modelling blood flow in patients with heart valve disease using deep learning: A computationally efficient method to expand diagnostic capabilities in clinical routine

Introduction

The computational modelling of blood flow is known to provide vital hemodynamic parameters for diagnosis and treatment-support for patients with valvular heart disease. However, most diagnosis/treatment-support solutions based on flow modelling proposed utilize time- and resource-intensive computational fluid dynamics (CFD) and are therefore difficult to implement into clinical practice. In contrast, deep learning (DL) algorithms provide results quickly with little need for computational power. Thus, modelling blood flow with DL instead of CFD may substantially enhances the usability of flow modelling-based diagnosis/treatment support in clinical routine. In this study, we propose a DL-based approach to compute pressure and wall-shear-stress (WSS) in the aorta and aortic valve of patients with aortic stenosis (AS).

Methods

A total of 103 individual surface models of the aorta and aortic valve were constructed from computed tomography data of AS patients. Based on these surface models, a total of 267 patient-specific, steady-state CFD simulations of aortic flow under various flow rates were performed. Using this simulation data, an artificial neural network (ANN) was trained to compute spatially resolved pressure and WSS using a centerline-based representation. An unseen test subset of 23 cases was used to compare both methods.

Results

ANN and CFD-based computations agreed well with a median relative difference between both methods of 6.0% for pressure and 4.9% for wall-shear-stress. Demonstrating the ability of DL to compute clinically relevant hemodynamic parameters for AS patients, this work presents a possible solution to facilitate the introduction of modelling-based treatment support into clinical practice.

Modelling the action potential propagation in a heart with structural heterogeneities: From high-resolution MRI to numerical simulations

Mathematical modelling and numerical simulation in cardiac electrophysiology have already been studied extensively. However, there is a clear lack of techniques and methodologies for studying the propagation of action potential in a heart with structural defects. In this article, we present a modified version of the bidomain model, derived using homogenisation techniques with the assumption of existence of diffusive inclusions in the cardiac tissue. The diffusive inclusions represent regions without electrically active myocytes, for example, fat, fibrosis, and so forth. We present an application of this model to a rat heart. Starting from high-resolution MRI, the geometry of the heart is built and meshed using image processing techniques. We perform a study of the effects of tissue heterogeneities induced by diffusive inclusions on the velocity and shape of the depolarisation wavefront. We present several test cases with different geometries of diffusive inclusions. We reach the conclusion that the conduction velocity is not affected in the best cases, while it is affected by up to 76% in the worst case scenario. Additionally, the shape of the wavefront was affected in some cases.

Segmentation of tongue shapes during vowel production in magnetic resonance images based on statistical modelling

Quantification of the anatomic and functional aspects of the tongue is pertinent to analyse the mechanisms involved in speech production. Speech requires dynamic and complex articulation of the vocal tract organs, and the tongue is one of the main articulators during speech production. Magnetic resonance imaging has been widely used in speech-related studies. Moreover, the segmentation of such images of speech organs is required to extract reliable statistical data. However, standard solutions to analyse a large set of articulatory images have not yet been established. Therefore, this article presents an approach to segment the tongue in two-dimensional magnetic resonance images and statistically model the segmented tongue shapes. The proposed approach assesses the articulator morphology based on an active shape model, which captures the shape variability of the tongue during speech production. To validate this new approach, a dataset of mid-sagittal magnetic resonance images acquired from four subjects was used, and key aspects of the shape of the tongue during the vocal production of relevant European Portuguese vowels were evaluated.

Fluid flow in porous media using image-based modelling to parametrize Richards' equation

The parameters in Richards' equation are usually calculated from experimentally measured values of the soil-water characteristic curve and saturated hydraulic conductivity. The complex pore structures that often occur in porous media complicate such parametrization due to hysteresis between wetting and drying and the effects of tortuosity. Rather than estimate the parameters in Richards' equation from these indirect measurements, image-based modelling is used to investigate the relationship between the pore structure and the parameters. A three-dimensional, X-ray computed tomography image stack of a soil sample with voxel resolution of 6 μm has been used to create a computational mesh. The Cahn-Hilliard-Stokes equations for two-fluid flow, in this case water and air, were applied to this mesh and solved using the finite-element method in COMSOL Multiphysics. The upscaled parameters in Richards' equation are then obtained via homogenization. The effect on the soil-water retention curve due to three different contact angles, 0°, 20° and 60°, was also investigated. The results show that the pore structure affects the properties of the flow on the large scale, and different contact angles can change the parameters for Richards' equation.

Image-based modelling of skeletal muscle oxygenation

The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, in particular for skeletal muscle during exercise. Disease is often associated with both an inhibition of the microvascular supply capability and is thought to relate to changes in the structure of blood vessel networks. Different methods exist to investigate the influence of the microvascular structure on tissue oxygenation, varying over a range of application areas, i.e. biological in vivo and in vitro experiments, imaging and mathematical modelling. Ideally, all of these methods should be combined within the same framework in order to fully understand the processes involved. This review discusses the mathematical models of skeletal muscle oxygenation currently available that are based upon images taken of the muscle microvasculature in vivo and ex vivo Imaging systems suitable for capturing the blood vessel networks are discussed and respective contrasting methods presented. The review further informs the association between anatomical characteristics in health and disease. With this review we give the reader a tool to understand and establish the workflow of developing an image-based model of skeletal muscle oxygenation. Finally, we give an outlook for improvements needed for measurements and imaging techniques to adequately investigate the microvascular capability for oxygen exchange.

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high-resolution (c. 5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare), with and without root hairs, were grown for 8 d in microcosms packed with sandy loam soil at 1.2 g cm-3 dry bulk density. Root hairs were visualised within air-filled pore spaces, but not in the fine-textured soil regions. We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore space between 0.8 and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image-based modelling.

On the importance of 3D, geometrically accurate, and subject-specific finite element analysis for evaluation of in-vivo soft tissue loads

Pressure ulcers are a type of local soft tissue injury due to sustained mechanical loading and remain a common issue in patient care. People with spinal cord injury (SCI) are especially at risk of pressure ulcers due to impaired mobility and sensory perception. The development of load improving support structures relies on realistic tissue load evaluation e.g. using finite element analysis (FEA). FEA requires realistic subject-specific mechanical properties and geometries. This study focuses on the effect of geometry. MRI is used for the creation of geometrically accurate models of the human buttock for three able-bodied volunteers and three volunteers with SCI. The effect of geometry on observed internal tissue deformations for each subject is studied by comparing FEA findings for equivalent loading conditions. The large variations found between subjects confirms the importance of subject-specific FEA.

A comparison of different approaches for imaging cracks in composites by X-ray microtomography

X-ray computed tomography (CT) has emerged as a key imaging tool in the characterization of materials, allowing three-dimensional visualization of an object non-destructively as well as enabling the monitoring of damage accumulation over time through time-lapse imaging. However, small defects and cracks can be difficult to detect, particularly in composite materials where low-contrast, plate-like geometries of large area can compromise detectability. Here, we investigate a number of strategies aimed at increasing the capability of X-ray CT to detect composite damage such as transverse ply cracking and delamination, looking specifically at a woven glass fibre-reinforced three-dimensional composite. High-resolution region of interest (ROI) scanning, in situ loading, phase contrast and contrast agents are examined systematically as strategies for improving the defect detectability. Spatial resolution, contrast, signal-to-noise ratio, full width at half maximum, user friendliness and measurement time are all considered. Taken together, the results suggest that high-resolution ROI scanning combined with the increased contrast resulting from staining give the highest defect detectability. This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.

Computational aspects of steel fracturing pertinent to naval requirements

Modern high strength and ductile steels are a key element of US Navy ship structural technology. The development of these alloys spurred the development of modern structural integrity analysis methods over the past 70 years. Strength and ductility provided the designers and builders of navy surface ships and submarines with the opportunity to reduce ship structural weight, increase hull stiffness, increase damage resistance, improve construction practices and reduce maintenance costs. This paper reviews how analytical and computational tools, driving simulation methods and experimental techniques, were developed to provide ongoing insights into the material, damage and fracture characteristics of these alloys. The need to understand alloy fracture mechanics provided unique motivations to measure and model performance from structural to microstructural scales. This was done while accounting for the highly nonlinear behaviours of both materials and underlying fracture processes. Theoretical methods, data acquisition strategies, computational simulation and scientific imaging were applied to increasingly smaller scales and complex materials phenomena under deformation. Knowledge gained about fracture resistance was used to meet minimum fracture initiation, crack growth and crack arrest characteristics as part of overall structural integrity considerations.

Multiscale modelling of hydraulic conductivity in vuggy porous media

Flow in both saturated and non-saturated vuggy porous media, i.e. soil, is inherently multiscale. The complex microporous structure of the soil aggregates and the wider vugs provides a multitude of flow pathways and has received significant attention from the X-ray computed tomography (CT) community with a constant drive to image at higher resolution. Using multiscale homogenization, we derive averaged equations to study the effects of the microscale structure on the macroscopic flow. The averaged model captures the underlying geometry through a series of cell problems and is verified through direct comparison to numerical simulations of the full structure. These methods offer significant reductions in computation time and allow us to perform three-dimensional calculations with complex geometries on a desktop PC. The results show that the surface roughness of the aggregate has a significantly greater effect on the flow than the microstructure within the aggregate. Hence, this is the region in which the resolution of X-ray CT for image-based modelling has the greatest impact.

Stochastic multi-scale prediction on the apparent elastic moduli of trabecular bone considering uncertainties of biological apatite (BAp) crystallite orientation and image-based modelling

An assessment of the mechanical properties of trabecular bone is important in determining the fracture risk of human bones. Many uncertainty factors contribute to the dispersion of the estimated mechanical properties of trabecular bone. This study was undertaken in order to propose a computational scheme that will be able to predict the effective apparent elastic moduli of trabecular bone considering the uncertainties that are primarily caused by image-based modelling and trabecular stiffness orientation. The effect of image-based modelling which focused on the connectivity was also investigated. A stochastic multi-scale method using a first-order perturbation-based and asymptotic homogenisation theory was applied to formulate the stochastically apparent elastic properties of trabecular bone. The effective apparent elastic modulus was predicted with the introduction of a coefficient factor to represent the variation of bone characteristics due to inter-individual differences. The mean value of the predicted effective apparent Young's modulus in principal axis was found at approximately 460 MPa for respective 15.24% of bone volume fraction, and this is in good agreement with other experimental results. The proposed method may provide a reference for the reliable evaluation of the prediction of the apparent elastic properties of trabecular bone.