Shape-driven deep neural networks for fast acquisition of aortic 3D pressure and velocity flow fields

Computational fluid dynamics (CFD) can be used to simulate vascular haemodynamics and analyse potential treatment options. CFD has shown to be beneficial in improving patient outcomes. However, the implementation of CFD for routine clinical use is yet to be realised. Barriers for CFD include high computational resources, specialist experience needed for designing simulation set-ups, and long processing times. The aim of this study was to explore the use of machine learning (ML) to replicate conventional aortic CFD with automatic and fast regression models. Data used to train/test the model consisted of 3,000 CFD simulations performed on synthetically generated 3D aortic shapes. These subjects were generated from a statistical shape model (SSM) built on real patient-specific aortas (N = 67). Inference performed on 200 test shapes resulted in average errors of 6.01% ±3.12 SD and 3.99% ±0.93 SD for pressure and velocity, respectively. Our ML-based models performed CFD in ∼0.075 seconds (4,000x faster than the solver). This proof-of-concept study shows that results from conventional vascular CFD can be reproduced using ML at a much faster rate, in an automatic process, and with reasonable accuracy.

Prévalence du SARS-CoV-2, étude sérologique en France chez des salariés non confinés et confinés

Objectifs: Evaluer rétrospectivement le taux de salariés, confinés (en télétravail) et non confinés, infectés par le SARS-CoV-2 après le 1^er confinement (Avril à Mai 2020).

Méthode: Un dépistage sérologique des anticorps anti-SARS-CoV-2, IgG et IgM, et un questionnaire sur leurs symptômes a été proposé aux 2090 salariés d’une même entreprise.

Résultats: La sérologie était positive pour 5,6% des 786 salariés inclus entre fin avril et juillet 2020 : 4,05% chez les non confinés, et 6,72%, chez les confinés (p=NS).

Parmi les positifs, 86,4% avaient présenté des symptômes, sans différence significative entre confinés et non confinés. Enfin, 1.7% des asymptomatiques étaient positifs.

Les symptômes n’étaient pas significativement différents entre les 2 groupes sauf pour l’anosmie-agueusie significativement plus fréquente dans le groupe des confinés.

Les symptômes significativement associés à une sérologie positive étaient l’anosmie-agueusie, la fièvre-sensation de fièvre-frissons, les courbatures, la fatigue malaise, un syndrome grippal et des symptômes respiratoires.

Ce faible taux de contamination peut être le résultat des mesures de prévention renforcées mises en place pour les salariés dès fin janvier 2020 par le Médecin du Travail pour limiter le risque de contamination au sein des locaux.

Conclusion: La prévalence du SARS-CoV-2 dans l’entreprise de fin avril à juillet 2020 était inférieure de moitié au taux rapporté dans la population d’Ile de France à la même période sans différence entre les salariés ayant poursuivi leur activité en présentiel par rapport aux confinés.

Automatic segmentation of the great arteries for computational hemodynamic assessment

BACKGROUND

Computational fluid dynamics (CFD) is increasingly used for the assessment of blood flow conditions in patients with congenital heart disease (CHD). This requires patient-specific anatomy, typically obtained from segmented 3D cardiovascular magnetic resonance (CMR) images. However, segmentation is time-consuming and requires expert input. This study aims to develop and validate a machine learning (ML) method for segmentation of the aorta and pulmonary arteries for CFD studies.

METHODS

90 CHD patients were retrospectively selected for this study. 3D CMR images were manually segmented to obtain ground-truth (GT) background, aorta and pulmonary artery labels. These were used to train and optimize a U-Net model, using a 70-10-10 train-validation-test split. Segmentation performance was primarily evaluated using Dice score. CFD simulations were set up from GT and ML segmentations using a semi-automatic meshing and simulation pipeline. Mean pressure and velocity fields across 99 planes along the vessel centrelines were extracted, and a mean average percentage error (MAPE) was calculated for each vessel pair (ML vs GT). A second observer (SO) segmented the test dataset for assessment of inter-observer variability. Friedman tests were used to compare ML vs GT, SO vs GT and ML vs SO metrics, and pressure/velocity field errors.

RESULTS

The network's Dice score (ML vs GT) was 0.945 (interquartile range: 0.929-0.955) for the aorta and 0.885 (0.851-0.899) for the pulmonary arteries. Differences with the inter-observer Dice score (SO vs GT) and ML vs SO Dice scores were not statistically significant for either aorta or pulmonary arteries (p = 0.741, p = 0.061). The ML vs GT MAPEs for pressure and velocity in the aorta were 10.1% (8.5-15.7%) and 4.1% (3.1-6.9%), respectively, and for the pulmonary arteries 14.6% (11.5-23.2%) and 6.3% (4.3-7.9%), respectively. Inter-observer (SO vs GT) and ML vs SO pressure and velocity MAPEs were of a similar magnitude to ML vs GT (p > 0.2).

CONCLUSIONS

ML can successfully segment the great vessels for CFD, with errors similar to inter-observer variability. This fast, automatic method reduces the time and effort needed for CFD analysis, making it more attractive for routine clinical use.

Computational investigation of the haemodynamics shows criticalities of central venous lines used for chronic haemodialysis in children

BACKGROUND

Haemodialysis is a life-saving treatment for children with kidney failure. The majority of children have haemodialysis through central venous lines (CVLs). The use of CVLs in pediatric patients is often associated to complications which can lead to their replacement. The aim of this study is to investigate haemodynamics of pediatric CVLs to highlight the criticalities of different line designs.

METHODS

Four models of CVLs for pediatric use were included in this study. The selected devices varied in terms of design and sizes (from 6.5 Fr to 14 Fr). Accurate 3D models of CVLs were reconstructed from high-resolution images including venous and arterial lumens, tips and side holes. Computational fluid dynamics (CFD) analyses were carried out to simulate pediatric working conditions of CVLs in ideal and anatomically relevant conditions.

RESULTS

The arterial lumens of all tested CVLs showed the most critical conditions with the majority of blood flowing through the side-holes. A zone of low flow was identified at the lines' tip. The highest shear stresses distribution (>10 Pa) was found in the 8 Fr line while the highest platelet lysis index in the 10 Fr model. The analysis on the anatomical geometry showed an increase in wall shear stress measured in the 10 F model compared to the idealised configuration. Similarly, in anatomical models an increased disturbance and velocity of the flow was found inside the vein after line placement.

CONCLUSION

This study provided a numerical characterization of fluid dynamics in pediatric CVLs highlighting performance criticalities (i.e. high shear stresses and areas of stagnation) associated to specific sizes (8 Fr and 10 Fr) and conditions (i.e. anatomical test).

Effects of Uncertainty of Outlet Boundary Conditions in a Patient-Specific Case of Aortic Coarctation

Computational Fluid Dynamics (CFD) simulations of blood flow are widely used to compute a variety of hemodynamic indicators such as velocity, time-varying wall shear stress, pressure drop, and energy losses. One of the major advances of this approach is that it is non-invasive. The accuracy of the cardiovascular simulations depends directly on the level of certainty on input parameters due to the modelling assumptions or computational settings. Physiologically suitable boundary conditions at the inlet and outlet of the computational domain are needed to perform a patient-specific CFD analysis. These conditions are often affected by uncertainties, whose impact can be quantified through a stochastic approach. A methodology based on a full propagation of the uncertainty from clinical data to model results is proposed here. It was possible to estimate the confidence associated with model predictions, differently than by deterministic simulations. We evaluated the effect of using three-element Windkessel models as the outflow boundary conditions of a patient-specific aortic coarctation model. A parameter was introduced to calibrate the resistances of the Windkessel model at the outlets. The generalized Polynomial Chaos method was adopted to perform the stochastic analysis, starting from a few deterministic simulations. Our results show that the uncertainty of the input parameter gave a remarkable variability on the volume flow rate waveform at the systolic peak simulating the conditions before the treatment. The same uncertain parameter had a slighter effect on other quantities of interest, such as the pressure gradient. Furthermore, the results highlight that the fine-tuning of Windkessel resistances is not necessary to simulate the post-stenting scenario.

A Proof of Concept of a Non-Invasive Image-Based Material Characterization Method for Enhanced Patient-Specific Computational Modeling

PURPOSE

Computational models of cardiovascular structures rely on their accurate mechanical characterization. A validated method able to infer the material properties of patient-specific large vessels is currently lacking. The aim of the present study is to present a technique starting from the flow-area (QA) method to retrieve basic material properties from magnetic resonance (MR) imaging.

METHODS

The proposed method was developed and tested, first, in silico and then in vitro. In silico, fluid-structure interaction (FSI) simulations of flow within a deformable pipe were run with varying elastic modules (E) between 0.5 and 32 MPa. The proposed QA-based formulation was assessed and modified based on the FSI results to retrieve E values. In vitro, a compliant phantom connected to a mock circulatory system was tested within MR scanning. Images of the phantom were acquired and post-processed according to the modified formulation to infer E of the phantom. Results of in vitro imaging assessment were verified against standard tensile test.

RESULTS

In silico results from FSI simulations were used to derive the correction factor to the original formulation based on the geometrical and material characteristics. In vitro, the modified QA-based equation estimated an average E = 0.51 MPa, 2% different from the E derived from tensile tests (i.e. E = 0.50 MPa).

CONCLUSION

This study presented promising results of an indirect and non-invasive method to establish elastic properties from solely MR images data, suggesting a potential image-based mechanical characterization of large blood vessels.

A workflow for patient-specific fluid-structure interaction analysis of the mitral valve: A proof of concept on a mitral regurgitation case

The mechanics of the mitral valve (MV) are the result of the interaction of different anatomical structures complexly arranged within the left heart (LH), with the blood flow. MV structure abnormalities might cause valve regurgitation which in turn can lead to heart failure. Patient-specific computational models of the MV could provide a personalised understanding of MV mechanics, dysfunctions and possible interventions. In this study, we propose a semi-automatic pipeline for MV modelling based on the integration of state-of-the-art medical imaging, i.e. cardiac magnetic resonance (CMR) and 3D transoesophageal-echocardiogram (TOE) with fluid-structure interaction (FSI) simulations. An FSI model of a patient with MV regurgitation was implemented using the finite element (FE) method and smoothed particle hydrodynamics (SPH). Our study showed the feasibility of combining image information and computer simulations to reproduce patient-specific MV mechanics as seen on medical images, and the potential for efficient in-silico studies of MV disease, personalised treatments and device design.

Patient-specific simulations for planning treatment in congenital heart disease

Patient-specific computational models have been extensively developed over the last decades and applied to investigate a wide range of cardiovascular problems. However, translation of these technologies into clinical applications, such as planning of medical procedures, has been limited to a few single case reports. Hence, the use of patient-specific models is still far from becoming a standard of care in clinical practice. The aim of this study is to describe our experience with a modelling framework that allows patient-specific simulations to be used for prediction of clinical outcomes. A cohort of 12 patients with congenital heart disease who were referred for percutaneous pulmonary valve implantation, stenting of aortic coarctation and surgical repair of double-outlet right ventricle was included in this study. Image data routinely acquired for clinical assessment were post-processed to set up patient-specific models and test device implantation and surgery. Finite-element and computational fluid dynamics analyses were run to assess feasibility of each intervention and provide some guidance. Results showed good agreement between simulations and clinical decision including feasibility, device choice and fluid-dynamic parameters. The promising results of this pilot study support translation of computer simulations as tools for personalization of cardiovascular treatments.

Metric field construction for anisotropic mesh adaptation with application to blood flow simulations

The goal of this paper is to generate an anisotropic metric field suitable for cardiovascular geometries before a fluid simulation. Starting from a curvature map, an initial surface metric field is computed. This metric is used for anisotropic surface mesh adaptation and consecutively extended inside the volume in a frontal manner. The algorithm is based on the method proposed by Alauzet but replaces the metric intersection steps by an original metric 'blending'. This allows for a graded anisotropic volume mesh with a refinement layer close to the walls. The benefits of the resulting mesh are multiple: a reduced number of degrees of freedom, a priori refinement in areas with strong gradients of velocity and automatically increased resolution in regions with high surface curvature. The primal application of this method is in the domain of cardiovascular flows. Flow fields and derived quantities (wall shear stress) through a model bypass around a stenosed artery obtained on an adapted and standard isotropic mesh are compared. In addition, the mesh generation method is tested on a more complex patient-specific geometry. Values of computed wall shear stress are shown to be close to values obtained on anisotropic Hessian-adapted mesh, demonstrating the computational efficiency of the approach in comparison with adaptation based on error indicators derived from flow field.

The 2.4-A crystal structure of the penicillin-resistant penicillin-binding protein PBP5fm from Enterococcus faecium in complex with benzylpenicillin

Penicillin-binding proteins (PBPs) are membrane proteins involved in the final stages of peptidoglycan synthesis and represent the targets of beta-lactam antibiotics. Enterococci are naturally resistant to these antibiotics because they produce a PBP, named PBP5fm in Enterococcus faecium, with low-level affinity for beta-lactams. We report here the crystal structure of the acyl-enzyme complex of PBP5fm with benzylpenicillin at a resolution of 2.4 A. A characteristic of the active site, which distinguishes PBP5fm from other PBPs of known structure, is the topology of the loop 451-465 defining the left edge of the cavity. The residue Arg464, involved in a salt bridge with the residue Asp481, confers a greater rigidity to the PBP5fm active site. In addition, the presence of the Val465 residue, which points into the active site, reducing its accessibility, could account for the low affinity of PBP5fm for beta-lactam. This loop is common to PBPs of low affinity, such as PBP2a from Staphylococcus aureus and PBP3 from Bacillus subtilis. Moreover, the insertion of a serine after residue 466 in the most resistant strains underlines even more the determining role of this loop in the recognition of the substrates.

French multicenter randomized double-blind placebo-controlled trial on nebulized amiloride in cystic fibrosis patients. The Amiloride-AFLM Collaborative Study Group

The effect of amiloride, a sodium channel blocker, has been evaluated in a multicenter randomized double-blind placebo-controlled trial in cystic fibrosis patients more than 5-years-old (n = 137) whose forced vital capacity (FVC), forced expiratory volume in 1 sec (FEV(1)), and forced mid-expiratory flow (FEF(25-75)) were not below 50%, 50%, and 30% of reference values, respectively. Patients were randomly allocated to two parallel groups. Sixty-four patients were chronically colonized with Pseudomonas aeruginosa; they received either amiloride or placebo as a nebulized solution three times daily for 6 months. Routine treatments were continued. Patients chronically colonized with Pseudomonas received nebulized colimycine twice a day for a month during the third and sixth months of treatment. Bronchopulmonary exacerbations were treated in the usual way. The effects of the amiloride treatment were assessed at the end of the 6-month treatment period. The effects on FVC and secondarily on FEV(1), FEF(25-75), the number of days on antibiotic therapy, the Shwachman score, a nutritional index (weight/height(2)), the change in sputum bacterial flora, and nocturnal cough were assessed. For the patients not chronically colonized with Pseudomonas, the effect of the treatment was also evaluated by counting chronic colonizations with pathogens appearing during the trial period. The present study failed to demonstrate any significant benefit of amiloride over placebo on FVC, FEV(1), and the other secondary endpoints in the studied population. Neither the chronically colonized, nor the noncolonized patients benefited. The confidence intervals of the differences between treatment groups indicated small differences that were most likely of no clinical significance. Complementary analyses taking into account the gender, the type of mutation, the subpopulations whose FVC and FEV(1) were below 80% of normal values at the beginning of the study, and also patients less than 10 years old, did not show any statistically or clinically significant improvements following amiloride therapy.

[Effectiveness and safety of hydroxyethyl-rutosides in the local treatment of symptoms of venous insufficiency during air travel]

During air travel, the length of time spent in a sitting position and the absence of muscular activity in the calves severely slow the rate of blood flow in the lower limbs. The aim of this randomized, cross-over, double-blind study was to evaluate local application of Hydroxyethyl-rutosides (O-Beta-Hydroxyethylrutosides) in the treatment of symptoms of venous insufficiency including stasis-induced edema during extended air travel on flights exceeding 6 hours. Hydroxyethyl-rutosides or placebo was applied every 3 or 4 hours throughout the flight. In the 51 subjects evaluated (both males and females) the results show statistically significant differences favoring treatment with Hydroxyethyl-rutosides both with regard to objective signs of edema: change in minimum ankle circumference was less during trips in which Hydroxyethyl-rutosides was applied, whether compared with the maximum measurement (p = 0.04) or the last measurement made during the flights, and with regard to subjective signs: several symptoms occurred significantly less frequently when the subject applied Hydroxyethyl-rutosides during the flight [pain (p = 0.03), sensation of heavy and tired legs (p = 0.04) and sensation of swelling (p = 0.02)]. the patient's overall assessment of the treatment was also favorable after using Hydroxyethyl-rutosides Gel (p = 0.01). the number of subjects complaining of edema (pitting edema, marks of shoes, difficulties putting shoes back on) was significantly lower during periods of treatment with Hydroxyethyl-rutosides Gel (p = 0.001). Local application of Hydroxyethyl-rutosides, 3 to 4 times during 6 to 14 hours is thus effective in treating the main symptoms of venous insufficiency including stasis-induced edema caused by extended periods in the sitting position during long air flights.

Arthroscopic evaluation of post-traumatic patellofemoral chondropathy

OBJECTIVE

To evaluate clinically and arthroscopically post-traumatic patellofemoral chondropathy.

METHODS

Fifty-nine patients with post-traumatic patellofemoral chondropathy were included in a cross sectional study and 46 of them completed a 6 month longitudinal study. Evaluation of the disease, performed once in the cross sectional study and twice (at entry and after 6 months) in the longitudinal study, included clinical and arthroscopic variables evaluating disease activity and severity. Arthroscopy was performed under local anesthesia in an outpatient procedure using a small arthroscope. Chondropathy was evaluated by the overall assessment of the investigator using a visual analog scale, and by the Société Française d'Arthroscopie (SFA) scoring system (SFA score: 0-100). Synovitis was assessed by the "synovitis score," which represents a composite index taking into account intensity, extent and location of synovial abnormalities.

RESULTS

In the cross sectional study, severity of chondropathy correlated with age, body mass index, disease duration, functional impairment (Lequesne's index and maximum number of steps descended), patellofemoral crepitus on active motion, limitation of flexion, and presence and amount of synovitis. Knee effusion correlated with the presence of synovitis, but no correlation was found between pain or functional impairment and presence or amount of synovitis. In the longitudinal study, no statistically significant change in chondropathy was observed after 6 months followup despite a statistically significant improvement in pain, function, and knee effusion after this period. However, a statistically significant correlation was found between the progression of patellofemoral chondropathy and the presence and amount of synovitis at baseline. Synovitis was present at baseline in 10 patients. Changes in SFA scores were 1.2 +/- 1.6 and -0.1 +/- 1.0 in the groups of patients with and without synovitis, respectively (p = 0.0062).

CONCLUSION

These data suggest that synovitis might have a deleterious effect on the evolution of post-traumatic patellofemoral chondropathy or might be a marker for active cartilage breakdown.