Stefano Gabriele

The Dof protein DAG1 mediates PIL5 activity on seed germination by negatively regulating GA biosynthetic gene AtGA3ox1

We have previously shown that inactivation of the gene encoding the Arabidopsis thaliana transcription factor DOF AFFECTING GERMINATION 1 (DAG1) renders seed germination more sensitive to both phytochrome B (phyB) and gibberellins (GA). dag1 mutant seeds require less red (R) light fluence and a lower GA concentration than WT to germinate. Here, we show that inactivation of the gene PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) results in down-regulation of DAG1. Inactivation of PIL5 in the dag1 mutant background further increased the germination potential of dag1 mutant seeds, supporting the suggestion that DAG1 is under the positive control of PIL5. Germination of dag1phyB seeds showed a reduced requirement of gibberellins as compared with phyB mutant seeds, both in the presence and in the absence of GA biosynthesis. Furthermore, the GA biosynthetic gene AtGA3ox1 is upregulated in dag1 seeds as compared with the WT, and DAG1 actually binds to the AtGA3ox1 promoter, as shown by chromatin immunoprecipitation experiments. Expression analysis at different time points confirms that AtGA3ox1 is directly regulated by DAG1, while suggesting that DAG1 is not a direct regulatory target of PIL5. Our data indicate that in the phyB pathway leading to seed germination, DAG1 negatively regulates GA biosynthesis and suggest that DAG1 acts downstream of PIL5. In addition, the analysis of hypocotyls of dag1 and phyB mutant plantlets, of plantlets overexpressing phyB in the dag1 mutant, as well as of dag1phyB double mutant suggests that DAG1 may act as a negative regulatory element downstream of phyB also in hypocotyl elongation.

4D-Analysis of Left Ventricular Heart Cycle Using Procrustes Motion Analysis

The aim of this study is to investigate human left ventricular heart morphological changes in time among 17 healthy subjects. Preliminarily, 2 patients with volumetric overload due to aortic insufficiency were added to our analyses. We propose a special strategy to compare the shape, orientation and size of cardiac cycle’s morphological trajectories in time. We used 3D data obtained by Speckle Tracking Echocardiography in order to detect semi-automated and homologous landmarks clouds as proxies of left ventricular heart morphology. An extended Geometric Morphometrics toolkit in order to distinguish between intra- and inter-individual shape variations was used. Shape of trajectories with inter-individual variation were compared under the assumption that trajectories attributes, estimated at electrophysiologically homologous times are expressions of left ventricular heart function. We found that shape analysis as commonly applied in Geometric Morphometrics studies fails in identifying a proper morpho-space to compare the shape of morphological trajectories in time. To overcome this problem, we performed a special type of Riemannian Parallel Transport, called “linear shift”. Whereas the two patients with aortic insufficiency were not differentiated in the static shape analysis from the healthy subjects, they set apart significantly in the analyses of motion trajectory’s shape and orientation. We found that in healthy subjects, the variations due to inter-individual morphological differences were not related to shape and orientation of morphological trajectories. Principal Component Analysis showed that volumetric contraction, torsion and twist are differently distributed on different axes. Moreover, global shape change appeared to be more correlated with endocardial shape change than with the epicardial one. Finally, the total shape variation occurring among different subjects was significantly larger than that observable across properly defined morphological trajectories.

A 1D higher gradient model derived from Koiter’s shell theory

A thin rectangular plate is modelled as an (initially flat) shell. Following Koiter, the two fundamental forms of the deformed middle surface are then used to define the strain measures of the body. On the middle surface of the plate two local coordinates are introduced: we will call them longitudinal and transversal, respectively. It is assumed that the components of the displacement field which characterize the middle surface kinematics can be expressed as a product of two functions: one defined along the longitudinal coordinate and one defined along the transversal coordinate. Given an explicit expression of the latter functions, the 2D plate fields are reduced to 1D ones. The functions of the transversal coordinate are chosen so that the stretch along it together with the membrane shear vanish. It is worth noting that the linearization of these constraints leads to the well-known Vlasov’s assumptions. It is shown that by modelling each side of a thin walled beam as a 1D continuum, the entire assembly can be reduced to a 1D model as well. This procedure gives rise to an hyperelastic 1D beam model in which at least the warping effect is taken into account. The main features of the model are shown by means of some simple applications.

An interval-based technique for FE model updating

Model updating techniques are largely used in civil and mechanical engineering to obtain reliable FE models. The model parameters are iteratively adjusted until the model response matches the measured structural response within a given tolerance. The task is made difficult by the uncertainty that affects both the structural response and the model parameters. In this work, the uncertainty is taken into account by a proper formulation of the problem in the framework of interval analysis. Uncertainty is replaced by interval numbers, functions are replaced by their thin or thick natural extension and the inclusion theorem is exploited to find the problem solution. Sample applications are illustrated using a modal representation of the structure. A numerical example is used to discuss the potential of the proposed method. A case study is solved to demonstrate the advantages of the method with respect to conventional updating techniques.

An Interval Uncertainty Based Method for Damage Identification

The problem of damage identification in presence of uncertainties is faced up in the framework of interval analysis. A method previously developed by the authors in the context of model updating and global minimization for dynamic problems is applied to identify the damage in framed structures. The inclusion property of the interval analysis is exploited to find the bounds of the physical solutions. Model parameters, experimental measures and modelling errors are considered as possible sources of uncertainty. The advantages of the interval approach are discussed through numerical simulations involving the different kind of uncertainties.

A New 4D Trajectory-Based Approach Unveils Abnormal LV Revolution Dynamics in Hypertrophic Cardiomyopathy

The assessment of left ventricular shape changes during cardiac revolution may be a new step in clinical cardiology to ease early diagnosis and treatment. To quantify these changes, only point registration was adopted and neither Generalized Procrustes Analysis nor Principal Component Analysis were applied as we did previously to study a group of healthy subjects. Here, we extend to patients affected by hypertrophic cardiomyopathy the original approach and preliminarily include genotype positive/phenotype negative individuals to explore the potential that incumbent pathology might also be detected. Using 3D Speckle Tracking Echocardiography, we recorded left ventricular shape of 48 healthy subjects, 24 patients affected by hypertrophic cardiomyopathy and 3 genotype positive/phenotype negative individuals. We then applied Generalized Procrustes Analysis and Principal Component Analysis and inter-individual differences were cleaned by Parallel Transport performed on the tangent space, along the horizontal geodesic, between the per-subject consensuses and the grand mean. Endocardial and epicardial layers were evaluated separately, different from many ecocardiographic applications. Under a common Principal Component Analysis, we then evaluated left ventricle morphological changes (at both layers) explained by first Principal Component scores. Trajectories’ shape and orientation were investigated and contrasted. Logistic regression and Receiver Operating Characteristic curves were used to compare these morphometric indicators with traditional 3D Speckle Tracking Echocardiography global parameters. Geometric morphometrics indicators performed better than 3D Speckle Tracking Echocardiography global parameters in recognizing pathology both in systole and diastole. Genotype positive/phenotype negative individuals clustered with patients affected by hypertrophic cardiomyopathy during diastole, suggesting that incumbent pathology may indeed be foreseen by these methods. Left ventricle deformation in patients affected by hypertrophic cardiomyopathy compared to healthy subjects may be assessed by modern shape analysis better than by traditional 3D Speckle Tracking Echocardiography global parameters. Hypertrophic cardiomyopathy pathophysiology was unveiled in a new manner whereby also diastolic phase abnormalities are evident which is more difficult to investigate by traditional ecocardiographic techniques.

Non-invasive assessment of functional strain lines in the real human left ventricle via speckle tracking echocardiography

A mechanics-based analysis of data from three-dimensional speckle tracking echocardiography is proposed, aimed at investigating deformations in myocardium and at assessing shape and function of distinct strain lines corresponding to the principal strain lines of the cardiac tissue. The analysis is based on the application of a protocol of measurement of the endocardial and epicardial principal strain lines, which was already tested on simulated left ventricles. In contrast with similar studies, it is established that endocardial principal strain lines cannot be identified with any structural fibers, not even along the systolic phase and is suggested that it is due to the capacity of the endocardial surface to contrast the dilation of the left ventricle.

Evaluation of the strain-line patterns in a human left ventricle: a simulation study.

The aim of this paper is to emphasise the role of the primary strain-line patterns in a human left ventricle (LV) within the complex system that is the heart. In particular, a protocol is proposed for the measurement of the principal strain lines (PSL) in the walls of the LV; this protocol is tested by means of a computational model which resembles a human LV. When the analysis is focused on the epicardial surface, PSL can be used to derive information on the directions of muscle fibres during the entire cardiac cycle, not only the systolic phase.

Homeostatic Left Heart integration and disintegration links atrio-ventricular covariation’s dyshomeostasis in Hypertrophic Cardiomyopathy

Left ventricle and left atrium are and have been practically always analyzed separately in common clinically and non-clinically oriented cardiovascular investigations. Both classic and speckle tracking echocardiographic data contributed to the knowledge about deformational impairments occurring in systo-diastolic differences. Recently new trajectory based approaches allowed a greater awareness about the entire left ventricle or left atrium revolution and on their deficiencies that take place in presence of hypertrophic cardiomyopathy. However, surprisingly, the concomitant function of the two left heart chambers has not been analyzed for their geometrical/mechanical relationship. For the first time we study here, by acquiring left ventricle and left atrial geometries on the same heartbeat, the trajectory attributes of the entire left heart treated as a whole shape and the shape covariation of its two subunits. We contrasted healthy subjects with patients affected by hypertrophic cardiomyopathy. We found impaired left heart trajectory mainly in terms of orientation and size. More importantly, we found profound differences in the direction of morphological covariation of left ventricle and left atrium. These findings open to new perspectives in pathophysiological evaluation of different diseases by allowing the appreciation of concomitant functioning of both left heart whole geometry and of its two chambers.

The TPS Direct Transport: A New Method for Transporting Deformations in the Size-and-Shape Space

Modern shape analysis allows the fine comparison of shape changes occurring between different objects. Very often the classic machineries of generalized Procrustes analysis and principal component analysis are used in order to contrast the shape change occurring among configurations represented by homologous landmarks. However, if size and shape data are structured in different groups thus constituting different morphological trajectories, a data centering is needed if one wants to compare solely the deformation representing the trajectories. To do that, inter-individual variation must be filtered out. This maneuver is rarely applied in studies using simulated or real data. A geometrical procedure named parallel transport, that can be based on various connection types, is necessary to perform such kind of data centering. Usually, the Levi Civita connection is used for interpolation of curves in a Riemannian space. It can also be used to transport a deformation. We demonstrate that this procedure does not preserve some important characters of the deformation, even in the affine case. We propose a novel procedure called ‘TPS Direct Transport’ which is able to perfectly transport deformation in the affine case and to better approximate non affine deformation in comparison to existing tools. We recommend to center shape data using the methods described here when the differences in deformation rather than in shape are under study.