Disc4All: 08 Early Stage Researcher (ESRs) positions 1029 views

The Marie Skłodowska-Curie Innovative Training Networks (ITN-ETN) is hiring early stage researchers (ESRs) for the project Training network to advance integrated computational simulations in translational medicine, applied to intervertebral disc degeneration: Disc4All. Disc4All aims to integrate available data and computational simulations on back pain caused by intervertebral disc degeneration with a multidisciplinary translational medicine approach.

About the project:

• The network will promote the interdisciplinary training of 15 predoctoral researchers in data processing and integration; experimental and theoretical/computer modelling; the development of computer algorithms; the generation of tools; and platforms of models and simulations for the transparent integration of primary data for clinical interpretation improved by models and simulations.
• Disc4All aims to tackle this issue through collaborative expertise of clinicians; computational physicists and biologists; geneticists; computer scientists; cell and molecular biologists; microbiologists; bioinformaticians; and industrial partners.
• It provides interdisciplinary training in data curation and integration; experimental and theoretical/computational modelling; computer algorithm development; tool generation; and model and simulation platforms to transparently integrate primary data for enhanced clinical interpretations through models and simulations.

Requirements:

• Mobility: to be eligible for a position, you should not have resided in the country of the host institution for more than 12 months over the three years before the starting date of the position, excluding holidays and (refugee status) asylum application.
• Early Stage Researcher (ESR): At the time of recruitment by the host organisation, an ESR shall be in the first four years (full-time equivalent research experience) of his/her research career and not have been awarded a doctoral degree.
• Candidates must prove that they fulfil the aforementioned criteria through relevant documentation (certificates, official statements, residency card, …).

OPEN POSITIONS:

1. ESR 1: Management of clinical, biological & simulated data for uniform simulation workflows​. The ESR 1 will exploit large research data infrastructure and will be responsible for the systematic treatment and machine interpretability of heterogeneous datasets (organ phenotype, patient condition, molecular signatures, sex & gender, psychological status, known comorbidities, …), to enable integration of data into holistic disease models and decision support systems. HOST: InSilicoTrials, Italy – Secondments: OULU; AQUAS; BSC-CNS – PhD delivered by: UPF – Deadline for recruitment: January 2021

Deadline: 31/10/2020

2. ESR 2: Integrated solvers for bidirectional coupling of physical & biological events over multiple scales. The ESR will work on creating models and algorithms for simulation of Intervertebral disc degeneration pathologies. The main task will be to develop a multiscale mechanistic modelling software by coupling an Agent Based (AB) simulation solver with a Finite Element(FE) solver for High Performance Computing. The Finite Element solver will be adapted to couple mechanical deformations and solute transport to perform osmoporoviscoelastic simulations, by using the processed MRI data of patient-specific disc geometries. The candidate will be expected to cover the following tasks: 1) Adapt the FE solver Alya to tackle solute transport simulations coupled with porous media finite deformations & with Donnan osmotic swelling; 2) Adapt AB solver Pandora to integrate regulation network and work with 3D meshes; 3) Couple Alya & Pandora over 3D meshes and generate a new multiscale AB-FE solver; 4) Verify and validate the multiscale solver & simulations; 5) Optimize for massive multiscale simulations on HPC; 6) Generate software package & provide initial support for integration into final platform – Host: BSC-CNS, Spain – Secondments: ULG; UBern – PhD delivered by: UPF – Deadline for recruitment: January 2021. Deadline: 30/09/2020
3. ESR 4: Classification of IVD radiological signs and relation with SNP & multi-omics profiles. The ESR 4 will focus on developing machine learning based prediction and severity assessment models for intervertebral disc (IVD) degeneration. The primary aim will be to combine radiomic features from magnetic resonance (MR) and X-ray images, omics data, and other background data of the patients – in order to discover multiple phenotypes of the IVD degenerative disease. In this project, we will leverage patient material from TwinsUK and Northern Finland Birth Cohort datasets. HOST: OULU, Finland – Secondments: Cluster UPF, BSC-CNS, GALGO; PLEXALIS – PhD delivered by: OULU – Deadline for recruitment: January 2021. Deadline: 31/10/2020​
4. ​ESR 5: 3D modelling of the lumbar spine & automatic extraction of 3D morphological features in LDD. ERS 5 will address 3D modelling of the lumbar spine from medical images. Methods using deep learning and statistical modelling will be developed to segment the lumbar vertebrae and intervertebral disks in 3D MRI sequences and CT image, and provide 3D subject-specific lumbar spine models from 2D medical images (X-rays or mid-sagital MR images) used in clinical practices. Those methods will be used in combination with finite-element-based simulation methods developed within other ESR14 and 15 to develop a diagnosis and predictive tool for intervertebral disk degeneration. HOST: GALGO, Spain – Secondments: OULU; InSilicoTrials – PhD delivered by: UPF – Deadline for recruitment: January 2021. Deadline: 15/09/2020​​ EXTENDED: 15/10/2020​​
5. ​ESR 6: GWAS & Microbiome associated with main IVD phenotypes. The ESR will provide initial seeds for gene prioritization as well as evidences about the validity of microbiome biomarkers in LDD, by exploiting the data from the TwinsUK and NFBC population cohorts. Candidate gene and GWAS-based approaches will be used to identify novel associations between gene variants and a variety of spine phenotypes. Bioinformatic methods will be further used for general confirmation. In particular, DisGeNET and genetic correlation with known risk factors for LDD will be interrogated. Additionally, the ESR will seek to address the question of whether the gut microbiome differs in people with Modic change. To do this, we will leverage existing MR scans available and collect stools (by post) in a process that has become routine in TwinsUK. HOST: KCL, United Kingdom – Secondments: IMIM, UPF – PhD delivered by: KCL. Deadline: 01/11/2020​
6. ​ESR 7: Experimental exploration of the microbiome in degenerated IVD. This doctoral research program will investigate the potential role of infective agents and the microbiome in low back pain. Utilising human intervertebral disc samples from surgery the IVD microbiome will be characterised together with associated microbiome sites using high throughput microbiome sequencing. In vitro co-culture systems will then be deployed to investigate the potential roles of infective agents and the microbiome on disc cell behaviour and implications in the pathogenesis of disc degeneration. Culture systems will be utilised which mimic the cellular niche of human intervertebral disc during disc degeneration. HOST: SHU, United Kingdom – Secondments: UBern; ULG – PhD delivered by: SHU. Deadline: 01/11/2020​
7. ​ESR 9: Standardized in vitro static modelling & mechanism- based analyses of gene /protein /SNP at the cell /tissue & organ levels. The contribution will consist of standardized in vitro static modelling & mechanism- based analyses of gene /protein / SNP at the cell /tissue & organ levels. The research will be to test physiological conditions using different pre-clinical 3D culture models. Laboratory methods involve qPCR, Western blotting, ELISA, immune-histology and microscopy but also biomechanical testing. HOST: UBern, Switzerland – Secondments: SHU; IMIM; RIT – PhD delivered by: UBern. SEE JOB OFFER & APPLY – Deadline: 20/09/2020
8. ​ESR 12: In vitro & In silico modelling of CEP degeneration mechanisms. ESR12 will be using the mesofluidics setup available at the host institute to test bovine IVD endplates under different fluid regimes defined through FE simulations with endplate micromodels by other partners in the consortium. Experiments consist of testing various biological conditions in the set-up and monitoring the tissue response through multiplex (elisa) and multi-omics (transcriptomics & metabolomics) assays. These experiments will serve to gain a system-level understanding of the interactions taking place in the IVD endplates and validate the computational models developed by other partners in the project. HOST: ULG, Belgium – Secondments: UBern; PAO; UPF – PhD delivered by: ULG. Deadline: 31/10/2020