Influence of Smoothing on Voxel-Based Mesh Accuracy in Micro-Finite Element

The interest in automatic volume meshing for finite element analysis (FEA) has grown more since the appearance of microfocus CT (μCT), due to its high resolution, which allows for the assessment of mechanical behaviour at a high precision. Nevertheless, the basic meshing approach of generating one hexahedron per voxel produces jagged edges. To prevent this effect, smoothing algorithms have been introduced to enhance the topology of the mesh. However, whether smoothing also improves the accuracy of voxel-based meshes in clinical applications is still under question. There is a trade-off between smoothing and quality of elements in the mesh. Distorted elements may be produced by excessive smoothing and reduce accuracy of the mesh. In the present work, influence of smoothing on the accuracy of voxel-based meshes in micro-FE was assessed. An accurate 3D model of a trabecular structure with known apparent mechanical properties was used as a reference model. Virtual CT scans of this reference model (with resolutions of 16, 32 and 64 μm) were then created and used to build voxel-based meshes of the microarchitecture. Effects of smoothing on the apparent mechanical properties of the voxel-based meshes as compared to the reference model were evaluated. Apparent Young’s moduli of the smooth voxel-based mesh were significantly closer to those of the reference model for the 16 and 32 μm resolutions. Improvements were not significant for the 64 μm, due to loss of trabecular connectivity in the model. This study shows that smoothing offers a real benefit to voxel-based meshes used in micro-FE. It might also broaden voxel-based meshing to other biomechanical domains where it was not used previously due to lack of accuracy. As an example, this work will be used in the framework of the European project ContraCancrum, which aims at providing a patient-specific simulation of tumour development in brain and lungs for oncologists. For this type of clinical application, such a fast, automatic, and accurate generation of the mesh is of great benefit.

Transcriptional silencing of nonsense codon-containing immunoglobulin micro genes requires translation of its mRNA

Eukaryotes have evolved quality control mechanisms that prevent the expression of genes in which the protein coding potential is crippled by the presence of a premature translation-termination codon (PTC). In addition to nonsense-mediated mRNA decay (NMD), a well documented posttranscriptional consequence of the presence of a PTC in an mRNA, we recently reported the transcriptional silencing of PTC-containing immunoglobulin (Ig) mu and gamma minigenes when they are stably integrated into the genome of HeLa cells. Here we demonstrate that this transcriptional silencing of PTC-containing Ig-mu constructs requires active translation of the cognate mRNA, as it is not observed under conditions where translation of the PTC-containing mRNA is inhibited through an iron-responsive element in the 5'-untranslated region. Furthermore, RNA interference-mediated depletion of the essential NMD factor Upf1 not only abolishes NMD but also reduces the extent of nonsense-mediated transcriptional gene silencing (NMTGS). Collectively, our data indicate that NMTGS and NMD are linked, relying on the same mechanism for PTC recognition, and that the NMTGS pathway branches from the NMD pathway at a step after Upf1 function.

Measuring the mechanical properties of plant cells by combining micro-indentation with osmotic treatments

Growth in plants results from the interaction between genetic and signalling networks and the mechanical properties of cells and tissues. There has been a recent resurgence in research directed at understanding the mechanical aspects of growth, and their feedback on genetic regulation. This has been driven in part by the development of new micro-indentation techniques to measure the mechanical properties of plant cells in vivo. However, the interpretation of indentation experiments remains a challenge, since the force measures results from a combination of turgor pressure, cell wall stiffness, and cell and indenter geometry. In order to interpret the measurements, an accurate mechanical model of the experiment is required. Here, we used a plant cell system with a simple geometry, Nicotiana tabacum Bright Yellow-2 (BY-2) cells, to examine the sensitivity of micro-indentation to a variety of mechanical and experimental parameters. Using a finite-element mechanical model, we found that, for indentations of a few microns on turgid cells, the measurements were mostly sensitive to turgor pressure and the radius of the cell, and not to the exact indenter shape or elastic properties of the cell wall. By complementing indentation experiments with osmotic experiments to measure the elastic strain in turgid cells, we could fit the model to both turgor pressure and cell wall elasticity. This allowed us to interpret apparent stiffness values in terms of meaningful physical parameters that are relevant for morphogenesis.

Comparison of Mixed and Kinematic Uniform Boundary Conditions in Homogenized Elasticity of Femoral Trabecular Bone Using Microfinite Element Analyses

Mechanical properties of human trabecular bone play an important role in age-related bone fragility and implant stability. Micro-finite element (microFE) analysis allows computing the apparent elastic properties of trabecular bone biopsies, but the results depend on the type of applied boundary conditions (BCs). In this study, 167 femoral trabecular cubic biopsies with a side length of 5.3 mm were analyzed using microFE analysis to compare their stiffness systematically with kinematic uniform boundary conditions (KUBCs) and periodicity-compatible mixed uniform boundary conditions (PMUBCs). The obtained elastic constants were then used in the volume fraction and fabric-based orthotropic Zysset-Curnier model to identify their respective model parameters. As expected, PMUBCs lead to more compliant apparent elastic properties than KUBCs, especially in shear. The differences in stiffness decreased with bone volume fraction and mean intercept length. Unlike KUBCs, PMUBCs were sensitive to heterogeneity of the biopsies. The Zysset-Curnier model predicted apparent elastic constants successfully in both cases with adjusted coefficients of determination of 0.986 for KUBCs and 0.975 for PMUBCs. The role of these boundary conditions in finite element analyses of whole bones and bone-implant systems will need to be investigated in future work.

The Interplay between Melting, Refertilization and Carbonatite Metasomatism in Off-Cratonic Lithospheric Mantle under Zealandia: an Integrated Major, Trace and Platinum Group Element Study

It is widely accepted that stabilization of the continental crust requires the presence of sub-continental lithospheric mantle. However, the degree of melt depletion required to stabilize the lithosphere and whether widespread refertilization is a significant process remain unresolved. Here, major and trace element, including platinum group elements (PGE), characterization of 40 mantle xenoliths from 13 localities is used to constrain the melt depletion, refertilization and metasomatic history of lithospheric mantle underneath the micro-continent Zealandia. Our previously published Re–Os isotopic data for a subset of these xenoliths indicate Phanerozoic to Paleoproterozoic ages and, reinterpreted with the new major and trace element data presented here, demonstrate that a large volume (>2 million km3) of lithospheric mantle with an age of 1·99 ± 0·21 Ga is present below the much younger crust of Zealandia. A peritectic melting model using moderately incompatible trace elements (e.g. Yb) in bulk-rocks demonstrates that these peridotites experienced a significant range of degrees of partial melting, between 3 and 28%. During subsolidus equilibration clinopyroxene gains significant rare earth elements (REE), which then leads to the underestimation of the degree of partial melting by ≤12% in fertile xenoliths. A new approach taking into account the effects of subsolidus re-equilibration on clinopyroxene composition effectively removes discrepancies in the calculated degree of melting and provides consistent estimates of between 4 and 29%. The estimated amount of melting is independent of the Re–Os model ages of the samples. The PGE patterns record simple melt depletion histories and the retention of primary base metal sulfides in the majority of the xenoliths. A rapid decrease in Pt/IrN observed at c. 1·0 wt % Al2O3 is a direct result of the exhaustion of sulfide in the mantle residue at c. 20–25% partial melting and the inability of Pt to form a stable alloy phase. Major elements preserve evidence for refertilization by a basaltic component that resulted in the formation of secondary clinopyroxene and low-forsterite olivine. The majority of xenoliths show the effects of cryptic metasomatic overprinting, ranging from minor to strong light REE enrichments in bulk-rocks (La/YbN = 0·16–15·9). Metasomatism is heterogeneous, with samples varying from those with weak REE enrichment and notable positive Sr and U–Th anomalies and negative Nb–Ta anomalies in clinopyroxene to those that have extremely high concentrations of REE, Th–U and Nb. Chemical compositions are consistent with a carbonatitic component contributing to the metasomatism of the lithosphere under Zealandia. Notably, the intense metasomatism of the samples did not affect the PGE budget of the peridotites as this was controlled by residual sulfides.