An efficient approach to converting three-dimensional image data into highly accurate computational models

Investigation of background, novelty and recent advance of iron (II,III) oxide- loaded on 3D polymer based scaffolds as regenerative implant for bone tissue engineering: A review

Bone tissue engineering had crucial role in the bone defects regeneration, particularly when allograft and autograft procedures have limitations. In this regard, different types of scaffolds are used in tissue regeneration as fundamental tools. In recent years, magnetic scaffolds show promising applications in different biomedical applications (in vitro and in vivo). As superparamagnetic materials are widely considered to be among the most attractive biomaterials in tissue engineering, due to long-range stability and superior bioactivity, therefore, magnetic implants shows angiogenesis, osteoconduction, and osteoinduction features when they are combined with biomaterials. Furthermore, these scaffolds can be coupled with a magnetic field to enhance their regenerative potential. In addition, magnetic scaffolds can be composed of various combinations of magnetic biomaterials and polymers using different methods to improve the magnetic, biocompatibility, thermal, and mechanical properties of the scaffolds. This review article aims to explain the use of magnetic biomaterials such as iron (II,III) oxide (Fe2O3 and Fe3O4) in detail. So it will cover the research background of magnetic scaffolds, the novelty of using these magnetic implants in tissue engineering, and provides a future perspective on regenerative implants.

Use of micro-CT to determine tracheobronchial airway geometries in three strains of mice used in inhalation toxicology as disease models

Aerosol dosimetry estimates for mouse strains used as models for human disease are not available, primarily because of the lack of tracheobronchial airway morphometry data. By using micro-CT scans of in-situ prepared lung casts, tracheobronchial airway morphometry for four strains of mice were obtained: Balb/c, AJ, C57BL/6, and Apoe^-/- . The automated tracheobronchial airway morphometry algorithms for airway length and diameter were successfully verified against previously published manual and automated tracheobronchial airway morphometry data derived from two identical in-situ Balb/c mouse lung casts. There was also excellent agreement in tracheobronchial airway length and diameter between the automated and manual airway data for the AJ, C57BL/6, and Apoe^-/- mice. Differences in branch angle measurements were partially due to the differences in definition between the automated algorithms and manual morphometry techniques. Unlike the manual airway morphometry techniques, the automated algorithms were able to provide a value for inclination to gravity for each airway. Inclusion of an inclination to gravity angle for each airway along with airway length, diameter, and branch angle make the current automated tracheobronchial airway data suitable for use in dosimetry programs that can provide dosimetry estimates for inhaled material. The significant differences in upper tracheobronchial airways between Balb/c mice and between C57BL/6 and Apoe^-/- mice highlight the need for mouse strain-specific aerosol dosimetry estimates.

Estimation of mass apparent density and Young's modulus of femoral neck-head region

The purpose of this study is to estimate mass apparent density and Young's modulus to investigate biomechanical properties of the proximal femur bone. In this study eleven specimens of sheep femur bone having age between 1-1.25 years and human femur bone having age between 14 and 81years are used. In the present study, the first technique attempts to estimate the density from the image-based Hounsfield unit which is obtained directly from a computed tomography image. The modulus of elasticity is estimated from density-elasticity relation which is available in the literature. Another technique is used to develop a correlation between computed apparent density and greyscale based coefficient obtained by material mapping method using commercial Simpleware ScanIP software. Estimated mean deviation in apparent mass density and Young's modulus is 4.34% and 4.69% in sheep bone and 4.35% and 4.94% in human bone respectively. It is found that apparent density and Young's modulus obtained shows close agreement with values reported in the literature. Moreover, the study attempts to build up a new material model between human and sheep for orthopaedics clinical trials and research in Indian context. In addition, it is also observed that bone mass density of sheep is 1.60 times human. This method can also be useful to study and analyse biomechanical properties of the human femur bone.

Image-based finite-element modeling of the human femur

Fracture is considered a critical clinical endpoint in skeletal pathologies including osteoporosis and bone metastases. However, current clinical guidelines are limited with respect to identifying cases at high risk of fracture, as they do not account for many mechanical determinants that contribute to bone fracture. Improving fracture risk assessment is an important area of research with clear clinical relevance. Patient-specific numerical musculoskeletal models generated from diagnostic images are widely used in biomechanics research and may provide the foundation for clinical tools used to quantify fracture risk. However, prior to clinical translation, in vitro validation of predictions generated from such numerical models is necessary. Despite adopting radically different models, in vitro validation of image-based finite element (FE) models of the proximal femur (predicting strains and failure loads) have shown very similar, encouraging levels of accuracy. The accuracy of such in vitro models has motivated their application to clinical studies of osteoporotic and metastatic fractures. Such models have demonstrated promising but heterogeneous results, which may be explained by the lack of a uniform strategy with respect to FE modeling of the human femur. This review aims to critically discuss the state of the art of image-based femoral FE modeling strategies, highlighting principal features and differences among current approaches. Quantitative results are also reported with respect to the level of accuracy achieved from in vitro evaluations and clinical applications and are used to motivate the adoption of a standardized approach/workflow for image-based FE modeling of the femur.

Computational Biomechanics: In-Silico Tools for the Investigation of Surgical Procedures and Devices

Biomechanical investigations of surgical procedures and devices are usually developed by means of human or animal models. The exploitation of computational methods and tools can reduce, refine, and replace (3R) the animal experimentations for scientific purposes and for pre-clinical research. The computational model of a biological structure characterizes both its geometrical conformation and the mechanical behavior of its building tissues. Model development requires coupled experimental and computational activities. Medical images and anthropometric information provide the geometrical definition of the computational model. Histological investigations and mechanical tests on tissue samples allow for characterizing biological tissues' mechanical response by means of constitutive models. The assessment of computational model reliability requires comparing model results and data from further experimentations. Computational methods allow for the in-silico analysis of surgical procedures and devices' functionality considering many different influencing variables, the experimental investigation of which should be extremely expensive and time consuming. Furthermore, computational methods provide information that experimental methods barely supply, as the strain and the stress fields that regulate important mechano-biological phenomena. In this work, general notes about the development of biomechanical tools are proposed, together with specific applications to different fields, as dental implantology and bariatric surgery.

High performance modeling of heterogeneous SOFC electrode microstructures using the MOOSE framework: ERMINE (Electrochemical Reactions in MIcrostructural NEtworks)

Electrochemical energy devices, such as batteries and fuel cells, contain active electrode components that have highly porous, multiphase microstructures for improved performance. Predictive electrochemical models of solid oxide fuel cell (SOFC) electrode performance based on measured microstructures have been limited to small length scales, a small number of simulations, and/or relatively homogeneous microstructures. To overcome the difficulty in modeling electrochemical activity of inhomogeneous microstructures at considerable length scales, we have developed a high-throughput simulation application that operates on high-performance computing platforms. The open-source application, named Electrochemical Reactions in MIcrostructural NEtworks (ERMINE), is implemented within the MOOSE computational framework, and solves species transport coupled to both three-phase boundary and two-phase boundary electrochemical reactions. As the core component, this application is further incorporated into a high-throughput computational workflow. The main advantages of the workflow include:•

Straightforward image-based volumetric meshing that conforms to complex, multi-phased microstructural features

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Computation of local electrochemical fields in morphology-resolved microstructures at considerable length scales

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Implementation on high performance computing platforms, leading to fast, high-throughput computations

Design and Fabrication of Random Metal Foam Structures for Laser Powder Bed Fusion

With the development of additive manufacturing, the building of new categories of lightweight structures such as random foams have been offered. Nevertheless, given the complexity of the required parts, macroscopic defects may result or the process may even fail. Therefore, proper actions must be taken at the design stage. In this paper, a method of design for additive manufacturing (DfAM) to build metal random foam structures is proposed. Namely, a procedure is suggested to generate a structure that has interconnected porosity. This procedure is based on the aimed fractional density and several technical requirements, and then the geometry is optimized and meshed. To validate the algorithm, a test article consisting of a metal cylinder with spherical random pores ranging from 1 to 6 mm in diameter with a resulting fractional density of 40 ± 2% has been conceived and manufactured by means of laser powder bed fusion (LPBF). On the basis of the outcome of the manufacturing process, crucial information has been gathered to update the algorithm.

Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): uncertainty quantification of geometric rupture risk parameters

Background

Geometric parameters have been proposed for prediction of cerebral aneurysm rupture risk. Predicting the rupture risk for incidentally detected unruptured aneurysms could help clinicians in their treatment decision. However, assessment of geometric parameters depends on several factors, including the spatial resolution of the imaging modality used and the chosen reconstruction procedure. The aim of this study was to investigate the uncertainty of a variety of previously proposed geometric parameters for rupture risk assessment, caused by variability of reconstruction procedures.

Materials

26 research groups provided segmentations and surface reconstructions of five cerebral aneurysms as part of the Multiple Aneurysms AnaTomy CHallenge (MATCH) 2018. 40 dimensional and non-dimensional geometric parameters, describing aneurysm size, neck size, and irregularity of aneurysm shape, were computed. The medians as well as the absolute and relative uncertainties of the parameters were calculated. Additionally, linear regression analysis was performed on the absolute uncertainties and the median parameter values.

Results

A large variability of relative uncertainties in the range between 3.9 and 179.8% was found. Linear regression analysis indicates that some parameters capture similar geometric aspects. The lowest uncertainties < 6% were found for the non-dimensional parameters isoperimetric ratio, convexity ratio, and ellipticity index. Uncertainty of 2D and 3D size parameters was significantly higher than uncertainty of 1D parameters. The most extreme uncertainties > 80% were found for some curvature parameters.

Conclusions

Uncertainty analysis is essential on the road to clinical translation and use of rupture risk prediction models. Uncertainty quantification of geometric rupture risk parameters provided by this study may help support development of future rupture risk prediction models.

Electronic supplementary material

The online version of this article (10.1186/s12938-019-0657-y) contains supplementary material, which is available to authorized users.

On the Development of Interspecies Traumatic Brain Injury Correspondence Rules

Traumatic brain injury analysis in human is exceedingly difficult due to the methods in which data can be collected, thus many researchers commonly implement animal surrogates. However, use of these surrogates is costly and restricted by ethical concerns and test logistics. Computational models and simulations do not have these constraints and can produce significant amounts of data in relatively short periods. This paper shows the development of a human head and neck model and a full body porcine model. Both models are developed from high-resolution CT and MRI scans and the latest low-to-high strain rate mechanical data available in the literature to represent tissue component material behaviors. Both models are validated against experiments from the literature and used to complete an initial interspecies correspondence rule development study for blast overpressure effects. The results indicate the similarities in the way injury develops in the pig brain and human brain but these similarities occur at very different insult levels. These results are extended by a study, which shows that blast peak pressure is the driving factor in injury prediction and, depending on the injury metric used, significantly different injuries could be predicted.

FEM Analysis of Dental Implant-Abutment Interface Overdenture Components and Parametric Evaluation of Equator® and Locator® Prosthodontics Attachments

The objective of this investigation was to analyze the mechanical features of two different prosthetic retention devices. By applying engineering tools like the finite element method (FEM) and Von Mises analyses, we investigated how dental implant devices hold out against masticatory strength during chewing cycles. Two common dental implant overdenture retention systems were analyzed and then compared with a universal—common dental abutment. The Equator^® attachment system and the Locator^® arrangement were processed using the FEM Ansys^® Workbench. The elastic features of the materials used in the study were taken from recent literature. Results revealed different responses for both the devices, and both systems guaranteed a perfect fit over the axial load. However, the different design and shape involves the customized use of each device for a typical clinical condition of applying overdenture systems over dental implants. The data from this virtual model showed different features and mechanical behaviors of the overdenture prosthodontics attachments. A three-dimensional system involved the fixture, abutment, and passant screws of three different dental implants that were created and analyzed. Clinicians should find the best prosthetic balance to better distribute the stress over the component, and to guarantee the patients clinical long-term results.

Finite-element analysis of microwave scattering from a three-dimensional human head model for brain stroke detection

In this paper, a detailed analysis of microwave (MW) scattering from a three-dimensional (3D) anthropomorphic human head model is presented. It is the first time that the finite-element method (FEM) has been deployed to study the MW scattering phenomenon of a 3D realistic head model for brain stroke detection. A major contribution of this paper is to add anatomically more realistic details to the human head model compared with the literature available to date. Using the MRI database, a 3D numerical head model was developed and segmented into 21 different types through a novel tissue-mapping scheme and a mixed-model approach. The heterogeneous and frequency-dispersive dielectric properties were assigned to brain tissues using the same mapping technique. To mimic the simulation set-up, an eight-elements antenna array around the head model was designed using dipole antennae. Two types of brain stroke (haemorrhagic and ischaemic) at various locations inside the head model were then analysed for possible detection and classification. The transmitted and backscattered signals were calculated by finding out the solution of the Helmholtz wave equation in the frequency domain using the FEM. FE mesh convergence analysis for electric field values and comparison between different types of iterative solver were also performed to obtain error-free results in minimal computational time. At the end, specific absorption rate analysis was conducted to examine the ionization effects of MW signals to a 3D human head model. Through computer simulations, it is foreseen that MW imaging may efficiently be exploited to locate and differentiate two types of brain stroke by detecting abnormal tissues' dielectric properties. A significant contrast between electric field values of the normal and stroke-affected brain tissues was observed at the stroke location. This is a step towards generating MW scattering information for the development of an efficient image reconstruction algorithm.

A Fully-Automated Subcortical and Ventricular Shape Generation Pipeline Preserving Smoothness and Anatomical Topology

In this paper, we present a fully-automated subcortical and ventricular shape generation pipeline that acts on structural magnetic resonance images (MRIs) of the human brain. Principally, the proposed pipeline consists of three steps: (1) automated structure segmentation using the diffeomorphic multi-atlas likelihood-fusion algorithm; (2) study-specific shape template creation based on the Delaunay triangulation; (3) deformation-based shape filtering using the large deformation diffeomorphic metric mapping for surfaces. The proposed pipeline is shown to provide high accuracy, sufficient smoothness, and accurate anatomical topology. Two datasets focused upon Huntington's disease (HD) were used for evaluating the performance of the proposed pipeline. The first of these contains a total of 16 MRI scans, each with a gold standard available, on which the proposed pipeline's outputs were observed to be highly accurate and smooth when compared with the gold standard. Visual examinations and outlier analyses on the second dataset, which contains a total of 1,445 MRI scans, revealed 100% success rates for the putamen, the thalamus, the globus pallidus, the amygdala, and the lateral ventricle in both hemispheres and rates no smaller than 97% for the bilateral hippocampus and caudate. Another independent dataset, consisting of 15 atlas images and 20 testing images, was also used to quantitatively evaluate the proposed pipeline, with high accuracy having been obtained. In short, the proposed pipeline is herein demonstrated to be effective, both quantitatively and qualitatively, using a large collection of MRI scans.

Micromechanical study of the load transfer in a polycaprolactone-collagen hybrid scaffold when subjected to unconfined and confined compression

Scaffolds are used in diverse tissue engineering applications as hosts for cell proliferation and extracellular matrix formation. One of the most used tissue engineering materials is collagen, which is well known to be a natural biomaterial, also frequently used as cell substrate, given its natural abundance and intrinsic biocompatibility. This study aims to evaluate how the macroscopic biomechanical stimuli applied on a construct made of polycaprolactone scaffold embedded in a collagen substrate translate into microscopic stimuli at the cell level. Eight poro-hyperelastic finite element models of 3D printed hybrid scaffolds from the same batch were created, along with an equivalent model of the idealized geometry of that scaffold. When applying an 8% confined compression at the macroscopic level, local fluid flow of up to 20 [Formula: see text]m/s and octahedral strain levels mostly under 20% were calculated in the collagen substrate. Conversely unconfined compression induced fluid flow of up to 10 [Formula: see text]m/s and octahedral strain from 10 to 35%. No relevant differences were found amongst the scaffold-specific models. Following the mechanoregulation theory based on Prendergast et al. (J Biomech 30:539-548, 1997. https://doi.org/10.1016/S0021-9290(96)00140-6 ), those results suggest that mainly cartilage or fibrous tissue formation would be expected to occur under unconfined or confined compression, respectively. This in silico study helps to quantify the microscopic stimuli that are present within the collagen substrate and that will affect cell response under in vitro bioreactor mechanical stimulation or even after implantation.

Modeling of ultrasonic wave propagation in composite laminates with realistic discontinuity representation

This paper presents a method for embedding realistic defect geometries of a fiber reinforced material in a finite element modeling environment in order to simulate active ultrasonic inspection. When ultrasonic inspection is used experimentally to investigate the presence of defects in composite materials, the microscopic defect geometry may cause signal characteristics that are difficult to interpret. Hence, modeling of this interaction is key to improve our understanding and way of interpreting the acquired ultrasonic signals. To model the true interaction of the ultrasonic wave field with such defect structures as pores, cracks or delamination, a realistic three dimensional geometry reconstruction is required. We present a 3D-image based reconstruction process which converts computed tomography data in adequate surface representations ready to be embedded for processing with finite element methods. Subsequent modeling using these geometries uses a multi-scale and multi-physics simulation approach which results in quantitative A-Scan ultrasonic signals which can be directly compared with experimental signals. Therefore, besides the properties of the composite material, a full transducer implementation, piezoelectric conversion and simultaneous modeling of the attached circuit is applied. Comparison between simulated and experimental signals provides very good agreement in electrical voltage amplitude and the signal arrival time and thus validates the proposed modeling approach. Simulating ultrasound wave propagation in a medium with a realistic shape of the geometry clearly shows a difference in how the disturbance of the waves takes place and finally allows more realistic modeling of A-scans.

Key developments that impacted the field of mechanobiology and mechanotransduction

Advances in mechanobiology have evolved through insights from multiple disciplines including structural engineering, biomechanics, vascular biology, and orthopaedics. In this paper, we reviewed the impact of key reports related to the study of applied loads on tissues and cells and the resulting signal transduction pathways. We addressed how technology has helped advance the burgeoning field of mechanobiology (over 33,600 publications from 1970 to 2016). We analyzed the impact of critical ideas and then determined how these concepts influenced the mechanobiology field by looking at the citation frequency of these reports as well as tracking how the overall number of citations within the field changed over time. These data allowed us to understand how a key publication, idea, or technology guided or enabled the field. Initial observations of how forces acted on bone and soft tissues stimulated the development of computational solutions defining how forces affect tissue modeling and remodeling. Enabling technologies, such as cell and tissue stretching, compression, and shear stress devices, allowed more researchers to explore how deformation and fluid flow affect cells. Observation of the cell as a tensegrity structure and advanced methods to study genetic regulation in cells further advanced knowledge of specific mechanisms of mechanotransduction. The future of the field will involve developing gene and drug therapies to simulate or augment beneficial load regimens in patients and in mechanically conditioning organs for implantation. Here, we addressed a history of the field, but we limited our discussions to advances in musculoskeletal mechanobiology, primarily in bone, tendon, and ligament tissues. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:605-619, 2018.

Bulging brains

Brain swelling is a serious condition associated with an accumulation of fluid inside the brain that can be caused by trauma, stroke, infection, or tumors. It increases the pressure inside the skull and reduces blood and oxygen supply. To relieve the intracranial pressure, neurosurgeons remove part of the skull and allow the swollen brain to bulge outward, a procedure known as decompressive craniectomy. Decompressive craniectomy has been preformed for more than a century; yet, its effects on the swollen brain remain poorly understood. Here we characterize the deformation, strain, and stretch in bulging brains using the nonlinear field theories of mechanics. Our study shows that even small swelling volumes of 28 to 56 ml induce maximum principal strains in excess of 30%. For radially outward-pointing axons, we observe maximal normal stretches of 1.3 deep inside the bulge and maximal tangential stretches of 1.3 around the craniectomy edge. While the stretch magnitude varies with opening site and swelling region, our study suggests that the locations of maximum stretch are universally shared amongst all bulging brains. Our model has the potential to inform neurosurgeons and rationalize the shape and position of the skull opening, with the ultimate goal to reduce brain damage and improve the structural and functional outcomes of decompressive craniectomy in trauma patients.

Levels of detail analysis of microwave scattering from human head models for brain stroke detection

In this paper, we have presented a microwave scattering analysis from multiple human head models. This study incorporates different levels of detail in the human head models and its effect on microwave scattering phenomenon. Two levels of detail are taken into account; (i) Simplified ellipse shaped head model (ii) Anatomically realistic head model, implemented using 2-D geometry. In addition, heterogenic and frequency-dispersive behavior of the brain tissues has also been incorporated in our head models. It is identified during this study that the microwave scattering phenomenon changes significantly once the complexity of head model is increased by incorporating more details using magnetic resonance imaging database. It is also found out that the microwave scattering results match in both types of head model (i.e., geometrically simple and anatomically realistic), once the measurements are made in the structurally simplified regions. However, the results diverge considerably in the complex areas of brain due to the arbitrary shape interface of tissue layers in the anatomically realistic head model.

After incorporating various levels of detail, the solution of subject microwave scattering problem and the measurement of transmitted and backscattered signals were obtained using finite element method. Mesh convergence analysis was also performed to achieve error free results with a minimum number of mesh elements and a lesser degree of freedom in the fast computational time. The results were promising and the E-Field values converged for both simple and complex geometrical models. However, the E-Field difference between both types of head model at the same reference point differentiated a lot in terms of magnitude. At complex location, a high difference value of 0.04236 V/m was measured compared to the simple location, where it turned out to be 0.00197 V/m. This study also contributes to provide a comparison analysis between the direct and iterative solvers so as to find out the solution of subject microwave scattering problem in a minimum computational time along with memory resources requirement.

It is seen from this study that the microwave imaging may effectively be utilized for the detection, localization and differentiation of different types of brain stroke. The simulation results verified that the microwave imaging can be efficiently exploited to study the significant contrast between electric field values of the normal and abnormal brain tissues for the investigation of brain anomalies. In the end, a specific absorption rate analysis was carried out to compare the ionizing effects of microwave signals to different types of head model using a factor of safety for brain tissues. It is also suggested after careful study of various inversion methods in practice for microwave head imaging, that the contrast source inversion method may be more suitable and computationally efficient for such problems.

The Influence of Porosity on Fatigue Crack Initiation in Additively Manufactured Titanium Components

Without post-manufacture HIPing the fatigue life of electron beam melting (EBM) additively manufactured parts is currently dominated by the presence of porosity, exhibiting large amounts of scatter. Here we have shown that the size and location of these defects is crucial in determining the fatigue life of EBM Ti-6Al-4V samples. X-ray computed tomography has been used to characterise all the pores in fatigue samples prior to testing and to follow the initiation and growth of fatigue cracks. This shows that the initiation stage comprises a large fraction of life (>70%). In these samples the initiating defect was often some way from being the largest (merely within the top 35% of large defects). Using various ranking strategies including a range of parameters, we found that when the proximity to the surface and the pore aspect ratio were included the actual initiating defect was within the top 3% of defects ranked most harmful. This lays the basis for considering how the deposition parameters can be optimised to ensure that the distribution of pores is tailored to the distribution of applied stresses in additively manufactured parts to maximise the fatigue life for a given loading cycle.

Mathematical and computational modelling of skin biophysics: a review

The objective of this paper is to provide a review on some aspects of the mathematical and computational modelling of skin biophysics, with special focus on constitutive theories based on nonlinear continuum mechanics from elasticity, through anelasticity, including growth, to thermoelasticity. Microstructural and phenomenological approaches combining imaging techniques are also discussed. Finally, recent research applications on skin wrinkles will be presented to highlight the potential of physics-based modelling of skin in tackling global challenges such as ageing of the population and the associated skin degradation, diseases and traumas.

Mesoscale Fracture Analysis of Multiphase Cementitious Composites Using Peridynamics

Concrete is a complex heterogeneous material, and thus, it is important to develop numerical modeling methods to enhance the prediction accuracy of the fracture mechanism. In this study, a two-dimensional mesoscale model is developed using a non-ordinary state-based peridynamic (NOSBPD) method. Fracture in a concrete cube specimen subjected to pure tension is studied. The presence of heterogeneous materials consisting of coarse aggregates, interfacial transition zones, air voids and cementitious matrix is characterized as particle points in a two-dimensional mesoscale model. Coarse aggregates and voids are generated using uniform probability distributions, while a statistical study is provided to comprise the effect of random distributions of constituent materials. In obtaining the steady-state response, an incremental and iterative solver is adopted for the dynamic relaxation method. Load-displacement curves and damage patterns are compared with available experimental and finite element analysis (FEA) results. Although the proposed model uses much simpler material damage models and discretization schemes, the load-displacement curves show no difference from the FEA results. Furthermore, no mesh refinement is necessary, as fracture is inherently characterized by bond breakages. Finally, a sensitivity study is conducted to understand the effect of aggregate volume fraction and porosity on the load capacity of the proposed mesoscale model.

Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion

Cytosolic crowding can influence the thermodynamics and kinetics of in vivo chemical reactions. Most significantly, proteins and nucleic acid crowders reduce the accessible volume fraction, ϕ, available to a diffusing substrate, thereby reducing its effective diffusion rate, Deff, relative to its rate in bulk solution. However, Deff can be further hindered or even enhanced, when long-range crowder/diffuser interactions are significant. To probe these effects, we numerically estimated Deff values for small, charged molecules in representative, cytosolic protein lattices up to 0.1 × 0.1 × 0.1 μm(3) in volume via the homogenized Smoluchowski electro-diffusion equation. We further validated our predictions against Deff estimates from ϕ-dependent analytical relationships, such as the Maxwell-Garnett (MG) bound, as well as explicit solutions of the time-dependent electro-diffusion equation. We find that in typical, moderately crowded cell cytoplasm (ϕ ≈ 0.8), Deff is primarily determined by ϕ; in other words, diverse protein shapes and heterogeneous distributions only modestly impact Deff. However, electrostatic interactions between diffusers and crowders, particularly at low electrolyte ionic strengths, can substantially modulate Deff. These findings help delineate the extent that cytoplasmic crowders influence small molecule diffusion, which ultimately may shape the efficiency and timing of intracellular signaling pathways. More generally, the quantitative agreement between computationally expensive solutions of the time-dependent electro-diffusion equation and its comparatively cheaper homogenized form suggest that the latter is a broadly effective model for diffusion in wide-ranging, crowded biological media.

New hybrid voxelized/analytical primitive in Monte Carlo simulations for medical applications

Monte Carlo simulations (MCS) applied in particle physics play a key role in medical imaging and particle therapy. In such simulations, particles are transported through voxelized phantoms derived from predominantly patient CT images. However, such voxelized object representation limits the incorporation of fine elements, such as artificial implants from CAD modeling or anatomical and functional details extracted from other imaging modalities. In this work we propose a new hYbrid Voxelized/ANalytical primitive (YVAN) that combines both voxelized and analytical object descriptions within the same MCS, without the need to simultaneously run two parallel simulations, which is the current gold standard methodology. Given that YVAN is simply a new primitive object, it does not require any modifications on the underlying MC navigation code. The new proposed primitive was assessed through a first simple MCS. Results from the YVAN primitive were compared against an MCS using a pure analytical geometry and the layer mass geometry concept. A perfect agreement was found between these simulations, leading to the conclusion that the new hybrid primitive is able to accurately and efficiently handle phantoms defined by a mixture of voxelized and analytical objects. In addition, two application-based evaluation studies in coronary angiography and intra-operative radiotherapy showed that the use of YVAN was 6.5% and 12.2% faster than the layered mass geometry method, respectively, without any associated loss of accuracy. However, the simplification advantages and differences in computational time improvements obtained with YVAN depend on the relative proportion of the analytical and voxelized structures used in the simulation as well as the size and number of triangles used in the description of the analytical object meshes.

An approach for patient-specific multi-domain vascular mesh generation featuring spatially varying wall thickness modeling

In this work, we present a computationally efficient image-derived volume mesh generation approach for vasculatures that implements spatially varying patient-specific wall thickness with a novel inward extrusion of the wall surface mesh. Multi-domain vascular meshes with arbitrary numbers, locations, and patterns of both iliac bifurcations and thrombi can be obtained without the need to specify features or landmark points as input. In addition, the mesh output is coordinate-frame independent and independent of the image grid resolution with high dimensional accuracy and mesh quality, devoid of errors typically found in off-the-shelf image-based model generation workflows. The absence of deformable template models or Cartesian grid-based methods enables the present approach to be sufficiently robust to handle aneurysmatic geometries with highly irregular shapes, arterial branches nearly parallel to the image plane, and variable wall thickness. The assessment of the methodology was based on i) estimation of the surface reconstruction accuracy, ii) validation of the output mesh using an aneurysm phantom, and iii) benchmarking the volume mesh quality against other frameworks. For the phantom image dataset (pixel size 0.105 mm; slice spacing 0.7 mm; and mean wall thickness 1.401±0.120 mm), the average wall thickness in the mesh was 1.459±0.123 mm. The absolute error in average wall thickness was 0.060±0.036 mm, or about 8.6% of the largest image grid spacing (0.7 mm) and 4.36% of the actual mean wall thickness. Mesh quality metrics and the ability to reproduce regional variations of wall thickness were found superior to similar alternative frameworks.

On the pressure response in the brain due to short duration blunt impacts

When the head is subject to non-penetrating (blunt) impact, contusion-type injuries are commonly identified beneath the impact site (the coup) and, in some instances, at the opposite pole (the contre-coup). This pattern of injury has long eluded satisfactory explanation and blunt head injury mechanisms in general remain poorly understood. There are only a small number of studies in the open literature investigating the head's response to short duration impacts, which can occur in collisions with light projectiles. As such, the head impact literature to date has focussed almost exclusively on impact scenarios which lead to a quasi-static pressure response in the brain. In order to investigate the response of the head to a wide range of impact durations, parametric numerical studies were performed on a highly bio-fidelic finite element model of the human head created from in vivo magnetic resonance imaging (MRI) scan data with non-linear tissue material properties. We demonstrate that short duration head impacts can lead to potentially deleterious transients of positive and negative intra-cranial pressure over an order of magnitude larger than those observed in the quasi-static regime despite reduced impact force and energy. The onset of this phenomenon is shown to be effectively predicted by the ratio of impact duration to the period of oscillation of the first ovalling mode of the system. These findings point to dramatically different pressure distributions in the brain and hence different patterns of injury depending on projectile mass, and provide a potential explanation for dual coup/contre-coup injuries observed clinically.

Workflow For Creating a Simulation Ready Virtual Population For Finite Element Modeling

Three dimensional image-based meshing of multipart structures from medical scan data continues to reveal exciting new possibilities for the application of simulation techniques to a wide range of biomedical problems. However, significant challenges to creating a population of simulation compatible models still exist. These include: 1) dataset availability—due to privacy rules and cost, very few readily available dataset repositories of human phantoms exist; 2) segmentation difficulty—segmentation of scan datasets is extremely man-hour intensive. Effort is often measured by months to years for a single model; 3) clean CAD model extraction—the faceted volumetric meshes and CAD geometry must contain conformal face mapping between touching objects. Since traditional part-by-part meshing approaches risk gaps or overlap between adjacent parts, manual and time consuming repair may be required. This paper demonstrates a potential solution to these challenges through a fast and efficient workflow that begins with newly available anatomical geometries, and culminates in a solved multi-object computational simulation. Using the new series of 4D extended cardiac-torso (XCAT) phantoms created by Segars et al., we use ScanIP (Simpleware Ltd., Exeter, UK) to convert these datasets into multi-object simulation ready geometry files that are imported into HFSS (ANSYS Inc., Canonsburg, PA) for EM simulation and analysis.

Irrigation of human prepared root canal--ex vivo based computational fluid dynamics analysis

AIM

To analyze the influence of the needle type, insertion depth, and irrigant flow rate on irrigant flow pattern, flow velocity, and apical pressure by ex-vivo based endodontic irrigation computational fluid dynamics (CFD) analysis.

METHODS

Human upper canine root canal was prepared using rotary files. Contrast fluid was introduced in the root canal and scanned by computed tomography (CT) providing a three-dimensional object that was exported to the computer-assisted design (CAD) software. Two probe points were established in the apical portion of the root canal model for flow velocity and pressure measurement. Three different CAD models of 27G irrigation needles (closed-end side-vented, notched open-end, and bevel open-end) were created and placed at 25, 50, 75, and 95% of the working length (WL). Flow rates of 0.05, 0.1, 0.2, 0.3, and 0.4 mL/s were simulated. A total of 60 irrigation simulations were performed by CFD fluid flow solver.

RESULTS

Closed-end side-vented needle required insertion depth closer to WL, regarding efficient irrigant replacement, compared to open-end irrigation needle types, which besides increased velocity produced increased irrigant apical pressure. For all irrigation needle types and needle insertion depths, the increase of flow rate was followed by an increased irrigant apical pressure.

CONCLUSIONS

The human root canal shape obtained by CT is applicable in the CFD analysis of endodontic irrigation. All the analyzed values -irrigant flow pattern, velocity, and pressure - were influenced by irrigation needle type, as well as needle insertion depth and irrigant flow rate.

On the mechanics of bacterial biofilms on non-dissolvable surgical sutures: a laser scanning confocal microscopy-based finite element study

Biofilms are bacterial communities encapsulated within a self-secreted extracellular polymeric substance and are responsible for a wide range of chronic medical device related infections. Understanding and addressing the conditions that lead to the attachment and detachment of biofilms from biomedical surfaces (orthopaedic implants, sutures, intravenous catheters, cardio-vascular stents) has the potential to identify areas of the device that might be more prone to infection and predict how and when biofilms might dislodge. In this study, an integrated software methodology was devised to create image-based microscopic finite element models of real biofilm colonies of Staphylococcus aureus attached to a fragment of surgical suture. The goal was to predict how deformation of the suture may lead to the potential detachment of biofilm colonies by solving the equations of continuum mechanics using the finite element method for various loading cases. Tension, torsion and bending of the biomaterial structure were simulated, demonstrating that small strains in the suture can produce surface shear stresses sufficient to trigger the sliding of biofilms over the suture surface. Applications of this technique to other medical devices are discussed.

The importance of lag screw position for the stabilization of trochanteric fractures with a sliding hip screw: a subject-specific finite element study

Using finite element analysis, we compared the biomechanical performance of a CT scan-based three-part trochanteric fracture model (31-A2 in the AO classification) stabilized with a sliding hip screw for nine different positions of the lag screw (3 × 3 arrangement, from anterior to posterior and from inferior to superior). Our results showed that the volume of bone susceptible to yielding in the head and neck region is the lowest for inferior positions and increases as the lag screw is moved superiorly. Overall, for this specific subject, the models less likely to lead to cut-out are the ones corresponding to inferior middle and inferior posterior positions of the lag screw. In our study, the tip-apex distance (TAD) was anti-correlated with the risk of cut-out, as quantified by the volume of bone susceptible to yielding, which suggests that a TAD >25 mm cannot be considered to be an accurate predictor of lag screw cut-out. Further clinical studies investigating lag screw cut-out should attempt to find more reliable predictors of cut-out that should better reflect the biomechanics and subject-specificity of the femoral head.

Patient-specific modelling of bone and bone-implant systems: the challenges

In the past three decades, finite element (FE) modelling has provided considerable understanding to the area of musculoskeletal biomechanics. However, most of this understanding has been generated using generic, standardised or idealised models. Patient-specific modelling (PSM) is almost never used for making clinical decisions. Imaging technologies have made it possible to create patient-specific geometries and FE meshes for modelling. While these have brought us closer to PSM, several challenges associated with the definition of material properties, loads, boundary conditions and interaction between components still need to be overcome. This study reviews the current status of PSM with respect to defining material behaviour and prescribing boundary conditions and interactions. With regard to the constitutive modelling of bone, it is seen that imaging is being increasingly used to define elastic properties (isotropic as well as anisotropic). However, the post-elastic and time-dependent behaviour, important for several modelling situations, is mostly obtained from in vitro experiments. Strain-based plasticity, not commonly available in FE codes, appears to have the potential of reducing an element of patient-specificity in modelling the yielding behaviour of bone. PSM of real boundary conditions that include muscles and ligaments continues to remain a challenge; many clinically relevant questions can be, however, answered without their inclusion. Simulation techniques to undertake PSM of interactions between bone and uncemented implants are available. Interference fit employed in both joint replacement fracture treatments induces considerable preload whose inclusion in models is important for the prediction of interface behaviour.

Accounting for patient variability in finite element analysis of the intact and implanted hip and knee: a review

It is becoming increasingly difficult to differentiate the performance of new joint replacement designs using available preclinical test methods. Finite element analysis is commonly used and the majority of published studies are performed on representative anatomy, assuming optimal implant placement, subjected to idealised loading conditions. There are significant differences between patients and accounting for this variability will lead to better assessment of the risk of failure. This review paper provides a comprehensive overview of the techniques available to account for patient variability. There is a brief overview of patient-specific model generation techniques, followed by a review of multisubject patient-specific studies performed on the intact and implanted femur and tibia. In particular, the challenges and limitations of manually generating models for such studies are discussed. To efficiently account for patient variability, the application of statistical shape and intensity models (SSIM) are being developed. Such models have the potential to synthetically generate thousands of representative models generated from a much smaller training set. Combined with the automation of the prosthesis implantation process, SSIM provides a potentially powerful tool for assessing the next generation of implant designs. The potential application of SSIM are discussed along with their limitations.

Biomechanics of the press-fit phenomenon in dental implantology: an image-based finite element analysis

Background

A fundamental pre-requisite for the clinical success in dental implant surgery is the fast and stable implant osseointegration. The press-fit phenomenon occurring at implant insertion induces biomechanical effects in the bone tissues, which ensure implant primary stability. In the field of dental surgery, the understanding of the key factors governing the osseointegration process still remains of utmost importance. A thorough analysis of the biomechanics of dental implantology requires a detailed knowledge of bone mechanical properties as well as an accurate definition of the jaw bone geometry.

Methods

In this work, a CT image-based approach, combined with the Finite Element Method (FEM), has been used to investigate the effect of the drill size on the biomechanics of the dental implant technique. A very accurate model of the human mandible bone segment has been created by processing high resolution micro-CT image data. The press-fit phenomenon has been simulated by FE analyses for different common drill diameters (D_A = 2.8 mm, D_B = 3.3 mm, and D_C = 3.8 mm) with depth L = 12 mm. A virtual implant model has been assumed with a cylindrical geometry having height L = 11 mm and diameter D = 4 mm.

Results

The maximum stresses calculated for drill diameters D_A, D_B and D_C have been 12.31 GPa, 7.74 GPa and 4.52 GPa, respectively. High strain values have been measured in the cortical area for the models of diameters D_A and D_B, while a uniform distribution has been observed for the model of diameter D_C . The maximum logarithmic strains, calculated in nonlinear analyses, have been ϵ = 2.46, 0.51 and 0.49 for the three models, respectively.

Conclusions

This study introduces a very powerful, accurate and non-destructive methodology for investigating the effect of the drill size on the biomechanics of the dental implant technique.

Further studies could aim at understanding how different drill shapes can determine the optimal press-fit condition with an equally distributed preload on both the cortical and trabecular structure around the implant.

Markerless Roentgen Stereophotogrammetric Analysis for in vivo implant migration measurement using three dimensional surface models to represent bone

Recent studies have shown that model-based RSA using implant surface models to detect in vivo migration is as accurate as the classical marker-based RSA method. Use of bone surface models would be a further advancement of the model-based method by decreasing complications arising from marker insertion. The aim of this pilot investigation was to assess the feasibility of a "completely markerless" model-based RSA in detecting migration of an implant using bone surface models instead of bone markers. A total knee arthroplasty (TKA) was performed on a human cadaver knee, which was subsequently investigated by repeated RSA measurements performed by one observer. The cadaver knee was CT scanned prior to implantation of the TKA. Tibia-fibular surface models were created using two different commercially available software packages to investigate the effect of segmentation software on the accuracy of repeated migration measures of zero displacement by one observer. Reverse engineered surface models of the TKA tibial component were created. The analysis of the RSA images was repeated 10 times by one individual observer. For the markerless method, the greatest apparent migration observed about the three anatomical axes investigated was between -2.08 and 1.35 mm (SD ≤ 0.88) for z-axis translation, and -4.57° to 7.86° (SD ≤ 3.17) for R(y)-axis rotation, which were well beyond out of the range of what is typically considered adequate for clinically relevant RSA measurements. Use of tibia-fibular surface models of the bone instead of markers could provide practical advantages in evaluating implant migration. However, we found the accuracy and precision of the markerless approach to be lower than that of marker-based RSA, to a degree which precludes the use of this method for measuring implant migration in its present form.

Flow characteristics in a canine aneurysm model: a comparison of 4D accelerated phase-contrast MR measurements and computational fluid dynamics simulations

PURPOSE

Our purpose was to compare quantitatively velocity fields in and around experimental canine aneurysms as measured using an accelerated 4D PC-MR angiography (MRA) method and calculated based on animal-specific CFD simulations.

METHODS

Two animals with a surgically created bifurcation aneurysm were imaged using an accelerated 4D PC-MRA method. Meshes were created based on the geometries obtained from the PC-MRA and simulations using "subject-specific" pulsatile velocity waveforms and geometries were then solved using a commercial CFD solver. Qualitative visual assessments and quantitative comparisons of the time-resolved velocity fields obtained from the PC-MRA measurements and the CFD simulations were performed using a defined similarity metric combining both angular and magnitude differences of vector fields.

RESULTS

PC-MRA and image-based CFD not only yielded visually consistent representations of 3D streamlines in and around both aneurysms, but also showed good agreement with regard to the spatial velocity distributions. The estimated similarity between time-resolved velocity fields from both techniques was reasonably high (mean value >0.60; one being the highest and zero being the lowest). Relative differences in inflow and outflow zones among selected planes were also reasonable (on the order of 10%-20%). The correlation between CFD-calculated and PC-MRA-measured time-averaged wall shear stresses was low (0.22 and 0.31, p < 0.001).

CONCLUSIONS

In two experimental canine aneurysms, PC-MRA and image-based CFD showed favorable agreement in intra-aneurismal velocity fields. Combining these two complementary techniques likely will further improve the ability to characterize and interpret the complex flow that occurs in human intracranial aneurysms.

Three-dimensional structure of the nasal passageway of a hagfish and its implications for olfaction

From high-resolution (65 μm) data acquired by magnetic resonance imaging, we have reconstructed the nasal passageway of a single adult hagfish specimen (probably Eptatretus stoutii). We have used this reconstruction to investigate how the anatomy and morphometry of the nasal passageway influence the olfactory ability of the hagfish. We found that the long, broad section of the passageway preceding the nasal chamber will delay the response to an odor by 1-2 s. Diffusion of odorant to the olfactory epithelium, on which the olfactory sensitivity of an animal depends, will be favored by the relatively large surface area of the olfactory epithelium (∼140 mm(2) ) and a modest expansion in the nasal chamber. Oscillating flow (0.3-0.4 Hz) within the narrow (65-130 μm) sensory channels of the nasal chamber is laminar (Reynolds number ∼ 5) and quasi-steady (Womersley number generally less than one). Distribution of flow over the olfactory epithelium may be aided by: (a) a narrowing before the nasal chamber; (b) partial blockage of the nasal passageway by a protrusion on the central olfactory lamella; and (c) the inward inclination of the olfactory lamellae.