PhD and postdoc opportunities - November 2024

Postdoc position within the EuroHPC project Dealii-X - an Exascale Framework for Digital Twins of the Human Body

Efficient numerical solution of multiphysics problems in biomedicine.

The SISSA dealii-X group is led by A. Cangiani and includes P. Africa and G. Rozza. The group is renowed for the development of polytopic FEMs and reduced order modelling and is involved in the modelling of the cardiovascular system. The postdoc will contribute to the efficient implementation and analysis of these powerful and flexible methods within the deal.II library for the solution of multiphysics and multiscale problems in complex domains. Tasks include:

• integration polytopic methods within the dealii-X meshing for exascale tools;
• exploitation general mesh methods as coarse solvers for complex multiscale problems.

The duration of the appointment is for 24 months, starting in early 2025. Monthly net salary around 2860€.

Deadline for applications January 7, 2025

More info HERE

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Estimation of fracture strength and bone fracture risk (femur) in rare diseases with the MEKANOS tool: the case of fibrous dysplasia of bone.
LYOS INSERM, LBMC Univ Eiffel, Lyon

Fibrous Dysplasia of Bone (FD) is a rare, benign, congenital (but non-hereditary) bone condition in which normal bone is replaced by fibrous-like tissue. This condition can cause bone pain, deformities, and fractures. The diagnosis is based on imaging and, if necessary, histopathological examination combined with genetic testing for the GNAS mutation. Treatment primarily focuses on pain management.

A significant unresolved issue for clinicians remains the evaluation of mechanical resistance and fracture risk in fibrous dysplasia lesions.The CEMOS (Expert Center for Bone Metastases) at the Cancer Institute of the Hospices Civils de Lyon (Professors Confavreux and Pialat) has developed the MEKANOS tool in collaboration with LYOS INSERM UMR1033 (H. Follet), LBMC UMR_T9406 (D. Mitton), and CREATIS (T. Grenier). MEKANOS is a numerical simulation tool designed to calculate the mechanical resistance of tumor-affected bones based on routine CT scans. It uses finite element analysis and applies specific loading conditions. Predictions of breaking resistance were made for patient images (Saillard et al., 2023), marking an additional step toward clinical application. Simultaneously, collaboration with CREATIS has automated bone segmentation, eliminating inter-operator variability.

The objective of MEKANOS is to provide clinicians with quantitative data to guide the management of bone metastases or myelomatous lesions in vertebrae or femurs (Confavreux, Cancers, 2021).

Mechanical characterisation of femoral cancellous bone samples with metastases
LBMC Univ Eiffel, LYOS INSERM-UCBL

Cancers such as lung or breast cancer can lead to secondary bone tumors, known as metastases. Bone metastases are responsible for complications in the form of severe pain requiring radiotherapy and can cause pathological fractures in long bones and vertebrae, frequently resulting in spinal cord compression.

Modeling studies using the finite element method, based on CT imaging, have been developed in collaboration between LYOS INSERM U1033 and LBMC UMR_T9406 to provide clinicians with quantitative data. In these models, the mechanical properties of each element are assigned based on density-elasticity relationships found in the literature, which are established from healthy bone without differentiating between healthy bone and metastatic tissue. Understanding the mechanical properties of metastases and the interface between metastases and healthy bone could improve the precision of these models.

Internship Objectives: to establish a mechanical testing protocol and characterize and compare the mechanical properties of femoral samples in healthy and pathological zones; to correlate microarchitectural parameters with the mechanical properties of femoral samples affected by metastases.

Expected Results: this project will identify changes in mechanical properties within the femur affected by metastases and their relationships with microarchitecture. The findings could contribute to improving numerical methods for predicting the resistance of bones affected by metastases.

Prediction of the failure strength of metastatic femurs with metastases: comparison between idealized and physiological loading conditions
LBMC Univ Eiffel, LYOS INSERM-UCBL

Cancers like lung and breast cancer often lead to bone metastases, which significantly reduce patients' quality of life due to complications such as fractures and restricted mobility. These issues affect about 50% of patients with bone metastases and have a significant socio-economic impact. Current clinical methods, like CT scans, provide qualitative insights but lack the precision needed to assess fracture risk effectively.

To address this, the LBMC and LYOS research teams are developing finite element (FE) models based on QCT scans to quantitatively predict femoral strength. A novel approach involves integrating patient-specific musculo-tendon forces into the models, as these forces impact local bone stress and strain, especially near muscle insertion points. This methodology also considers non-optimal muscle control scenarios, such as muscle weakness or joint pain, which could increase fracture risk.

Internship Objectives: Apply musculo-tendon forces from a musculoskeletal model to FE femur models. Assess how physiological loading affects strain distribution and bone strength compared to idealized loading. Simulate non-optimal muscle control to explore variations in joint and muscle loads.

Methodology:

• Reconstruct 3D femur models from QCT scans and incorporate musculo-tendon forces using laboratory tools.
• Simulate various muscle force distributions and analyze their impact on bone strength.
• Compare results under different physiological and idealized loading conditions. Expected Outcomes:

Expected Outcomes: The project aims to enhance fracture risk prediction by integrating physiological data into FE models, helping clinicians choose optimal treatments for patients with bone metastases.

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Assessment of the fracture risk of femurs with metastases using subject-specific biomechanical models: longitudinal patients followup

LBMC Univ Eiffel, LYOS INSERM-UCBL

Cancers such as lung or breast cancer can lead to secondary tumors in the bone, known as metastases. Bone metastases are responsible for complications such as severe pain requiring radiotherapy and can cause pathological fractures of long bones and vertebrae, often resulting in spinal cord compression. Currently, most patients with bone metastases at risk of fracture undergo a CT scan focused on the lesion to better characterize its extent and location. However, this examination remains qualitative.

Modeling work using the finite element method, based on CT imaging, has been developed by the LYOS INSERM U1033 and the LBMC UMR_T9406 to provide clinicians with quantitative data. This method has been evaluated on experimental ex vivo data from various international laboratories, including LYOS and LBMC (Gardegaront et al., 2024). In collaboration with the CREATIS laboratory, bone segmentation has been automated to eliminate inter-operator variability. Predictions of fracture resistance have been performed on patient images (Saillard et al., 2024). Moreover, phantom-less calibration methods have been evaluated using standardized calibrated CT images.

Objectives of the Internship: To apply the numerical simulation method developed in Lyon (by LYOS, LBMC, and CREATIS) to patient CT images (both calibrated and non-calibrated). To compare the fracture risk predicted by the model with the occurrence or non-occurrence of fractures.

Expected Results: This project will contribute to the application of numerical methods for predicting the strength of bones with metastases using patient data with longitudinal follow-up. This internship will play a critical role in validating these personalized biomechanical models to assist clinicians in managing patients.

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Mechanical characterization for 3D printing of vertebrae with or without bone metastases

LBMC Univ Eiffel, LYOS INSERM-UCBL

The most common cancers, such as breast, lung, and prostate cancers, often cause bone metastases that spread from the primary tumor site to the bones. These metastases can cause severe pain and weaken the bone structure, increasing the risk of spinal fractures. Currently, clinicians assess spinal stability using the SINS (Spinal Instability Neoplastic Score), which is based on morphological and clinical parameters. This score helps clinicians decide between treating the metastasis or stabilizing the spine through surgery.

Numerical modeling appears to be a relevant tool to estimate the fracture load of a vertebra based on clinical imaging data. INSERM Unit U1033 (LYOS) has conducted research on osteoporotic and metastatic bones using finite element simulations that integrate bone geometry, material properties (cortical/spongy bone and metastasis), and loading conditions [2]. These models are usually validated through experiments on human anatomical specimens. However, these approaches remain time- and resource-intensive.

The overall goal of this project is to develop 3D physical vertebra models through additive manufacturing (MatéIS). The aim of this project is to create a clinically usable model using clinical imaging data with limited resolution (voxel > 400 µm), which does not allow the segmentation of the trabecular bone network. These 3D-printed physical models will be validated through mechanical testing on human vertebrae using a collection of human vertebrae available at LYOS.

Internship Objective: to evaluate the anisotropic mechanical properties of the 3D-printed TPMS architecture through mechanical testing and numerical simulations, with the goal of integrating these findings into the design of the 3D-printed physical model.

Expected Results: This project will verify the feasibility of creating a 3D-printed vertebra model that reproduces the global behavior of a human vertebra under loading.