Data for: Numerical modelling and comparison of the temporal evolution of mantle and tails surrounding rigid elliptical objects in simple shear regime under stick and slip boundary conditions

Structures associated with rigid inclusions are a rich source of evidence to understand the local deformation regime. The behaviour of rigid objects in modelled here as being immersed in a linear Newtonian fluid with either (i) a stick boundary condition (continuity of stress and velocity across the boundary) or (ii) a slip boundary condition (continuity of boundary normal stress and velocity across the boundary with zero shear stress at the boundary). Of particular interest are the types of structures developed in a concentric region adjacent to the object termed the mantle. A model of the displacement of points around the inclusion comprises a set of ordinary differential equations which are solved numerically. A comprehensive set of simulations for a variety of mantle sizes, object aspect ratios, initial orientations as well as different boundary conditions has been performed. A comparison between natural examples and model output indicates a level of consistency. The resulting structures differ in detail and in a broader sense. In general $\delta$-type structures only develop when stick boundary conditions are in operation. In contrast, $\sigma$-type structures at high strain are restricted to slip boundary conditions. Slip conditions also tends to be the source of complex mantle types involving more than one generation of mantle structures or wings. Furthermore, our model indicates that using asymmetry of orientation of objects relative to the shear direction may be problematic when used alone, particularly if stick boundary conditions prevail but that together with mantle structures there is less chance of confusion

Data for: Numerical modelling and comparison of the temporal evolution of mantle and tails surrounding rigid elliptical objects in simple shear regime under stick and slip boundary conditions

Structures associated with rigid inclusions are a rich source of evidence to understand the local deformation regime. The behaviour of rigid objects in modelled here as being immersed in a linear Newtonian fluid with either (i) a stick boundary condition (continuity of stress and velocity across the boundary) or (ii) a slip boundary condition (continuity of boundary normal stress and velocity across the boundary with zero shear stress at the boundary). Of particular interest are the types of structures developed in a concentric region adjacent to the object termed the mantle. A model of the displacement of points around the inclusion comprises a set of ordinary differential equations which are solved numerically. A comprehensive set of simulations for a variety of mantle sizes, object aspect ratios, initial orientations as well as different boundary conditions has been performed. A comparison between natural examples and model output indicates a level of consistency. The resulting structures differ in detail and in a broader sense. In general $\delta$-type structures only develop when stick boundary conditions are in operation. In contrast, $\sigma$-type structures at high strain are restricted to slip boundary conditions. Slip conditions also tends to be the source of complex mantle types involving more than one generation of mantle structures or wings. Furthermore, our model indicates that using asymmetry of orientation of objects relative to the shear direction may be problematic when used alone, particularly if stick boundary conditions prevail but that together with mantle structures there is less chance of confusion.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Animal models of pulmonary hypertension: Getting to the heart of the problem.

Despite recent therapeutic advances, pulmonary hypertension (PH) remains a fatal disease due to the development of right ventricular (RV) failure. At present, no RV-targeted therapies are available, and RV function is not widely considered in the preclinical assessment of new therapeutics. Several small animal models are used in the study of PH, including the classic models of exposure to either hypoxia or monocrotaline, newer combinational and genetic models, and pulmonary artery banding, a surgical model of pure RV pressure overload. These models recapitulate selected features of the structural remodelling and functional decline seen in patients and have provided valuable insight into the pathophysiology of RV failure. However, significant reversal of remodelling and improvement in RV function remains a therapeutic obstacle. Emerging animal models will provide a deeper understanding of the mechanisms governing the transition from adaptive remodelling to a failing RV, aiding the hunt for druggable molecular targets

Guaranteed ellipse fitting with the Sampson distance

When faced with an ellipse fitting problem, practitioners frequently resort to algebraic ellipse fitting methods due to their simplicity and efficiency. Currently, practitioners must choose between algebraic methods that guarantee an ellipse fit but exhibit high bias, and geometric methods that are less biased but may no longer guarantee an ellipse solution. We address this limitation by proposing a method that strikes a balance between these two objectives. Specifically, we propose a fast stable algorithm for fitting a guaranteed ellipse to data using the Sampson distance as a data-parameter discrepancy measure. We validate the stability, accuracy, and efficiency of our method on both real and synthetic data. Experimental results show that our algorithm is a fast and accurate approximation of the computationally more expensive orthogonal-distance-based ellipse fitting method. In view of these qualities, our method may be of interest to practitioners who require accurate and guaranteed ellipse estimates.Zygmunt L. Szpak, Wojciech Chojnacki and Anton van den Henge

Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions

Background Cryo-electron tomography (cryo-ET) enables 3D imaging of macromolecular structures. Reconstructed cryo-ET images have a “missing wedge” of data loss due to limitations in rotation of the mounting stage. Most current approaches for structure determination improve cryo-ET resolution either by some form of sub-tomogram averaging or template matching, respectively precluding detection of shapes that vary across objects or are a priori unknown. Various macromolecular structures possess polyhedral structure. We propose a classification method for polyhedral shapes from incomplete individual cryo-ET reconstructions, based on topological features of an extracted polyhedral graph (PG). Results We outline a pipeline for extracting PG from 3-D cryo-ET reconstructions. For classification, we construct a reference library of regular polyhedra. Using geometric simulation, we construct a non-parametric estimate of the distribution of possible incomplete PGs. In studies with simulated data, a Bayes classifier constructed using these distributions has an average test set misclassification error of?<?5 % with upto 30 % of the object missing, suggesting accurate polyhedral shape classification is possible from individual incomplete cryo-ET reconstructions. We also demonstrate how the method can be made robust to mis-specification of the PG using an SVM based classifier. The methodology is applied to cryo-ET reconstructions of 30 micro-compartments isolated from E. coli bacteria. Conclusions The predicted shapes aren’t unique, but all belong to the non-symmetric Johnson solid family, illustrating the potential of this approach to study variation in polyhedral macromolecular structures