PhD Project D-Risc:
Multiscale modelling & data mining for intervertebral disc degeneration
risk prediction
(Pompeu Fabra
University, Barcelona, Spain)
GRANT PROGRAMME: “LA CAIXA” DOCTORATE INPHINIT
35 PhD fellowships for early-stage researchers of any nationality to
pursue their PhD studies in research centres accredited with the Spanish Seal
of Excellence Severo Ochoa, María de Maeztu or Health Institute Carlos III.
This frame is addressed exclusively to PhD research projects on STEM
disciplines: life sciences and health, experimental sciences, physics,
chemistry and mathematics.
More
information
POSITION: “D-Risc: Multiscale modelling & data mining for intervertebral disc degeneration risk prediction“
Area and discipline: please
choose 1 from the following list:
Area of knowledge
Physical Sciences, Mathematics and Engineering
Group of disciplines
Telecommunications, Electronics, Robotics,
Biomedical Engineering, Automation Engineering, ICT
Discipline
Biomedical Engineering, ICT
Research project / Research
Group description:
Research
project and main focus of the research line of the research group in which the
fellow would join
D-Risc aims to reveal critical interplays of crucial stimuli within the
intervertebral disc (IVD) that might lead to IVD degeneration, based on
morphological and physiological parameters. Different models at the organ,
tissue and cellular levels will be used. Specifically, the project will combine
multi-physics finite element models at the organ and tissue levels with
agent-based and network models at the cell and molecular levels, to simulate
the local regulation of IVD cells in multifactorial physical and biochemical
micro-environments. Simulation results will be mined with patient-specific
morphological, physical activity and life-style data. Depending on the
identified multiscale paths that can lead to degeneration-related cell activity
(i.e. catabolic shift of cell activity), personalised recommendations for
prevention- and optimised conservative treatments will be established.
D-Risc will exploit the competencies of the Biomechanics and
Mechanobiology (BMMB – http://biomech.es) lab of the BCN MedTech research unit at the Department of Information
and Communication Technologies (DTIC) of the Universitat Pompeu Fabra (UPF),
Barcelona. The project will be additionally implemented in cooperation with the
medical image analysis and machine learning areas of BCN MedTech (http://bcn-medtech.upf.edu/).
UPF was established in 1990 as a public university with strong
dedication to excellence in research and teaching. It is the 1st Spanish
university in the world Top 200 (THE2020), the 11th (ranked 5th in Europe and
1st in Spain) under 50 years (THE18). It also ranked 5th in Europe and 1st in
Spain (U-Multirank 2018) in teaching and research performance (U-Ranking, BBVA
Foundation & Ivie, 2018), quality output (excellence rate), normalized
impact and percentage of collaborative papers with foreign institutions. UPF is
full member of the Big Data Value Association (BDVA). DTIC has since its
creation emphasized scientific excellence and internationalisation as core
aspects of its activities. It has an important track record of active
participation in EU projects (a total of 66 FP7 projects and 10 other projects
in non-FP7 program such as CIP, Ambient Assisted Living and the Lifelong
Learning Program, and, up to now 44 H2020 projects). It is the Spanish
university department with the largest number of ERC grants (9 FP7 and 9 H2020)
and is part of the FET Flagship initiative “The Human Brain Project”. DTIC has
been awarded the “María de Maeztu” excellence by the Spanish government for the
quality and relevance of its pioneering scientific research.
BCN MedTech is the Barcelona Centre for New Medical Technologies at UPF.
It focusses on biomedical integrative research, including mathematical and
computational models, algorithms and systems for computer-aided diagnosis and
treatment, and the translation thereof into relevant clinical problems and
industrial products. It has a team of 60 full time researchers working on
medical image and signal processing, computational simulation,
computer-assisted surgery and biomedical electronics. Within BCN MedTech, the
BMMB lab combines mechanistic and stochastic theoretical modelling with
computational methods in biology and physics, to rationally explore the complex
multiscale interactions between tissue multiphysics and biological processes,
and to understand the bottom-up regulation of the functional biomechanics of
organs in health and disease. The specific targets are cartilaginous (rheumatic
disorders), bone (osteoporosis), arterial (atherosclerosis) and lung
(emphysema) tissues. The project will combine this expertise with computational
anatomy and manifold learning techniques for patient stratification, from the
BCN MedTech medical image analysis and machine learning areas.
Job
position description: role, responsibilities and skills required within the
project/group.
D-Risc
capitalizes on previous research at BCN MedTech, to assess the risk of disc
degeneration (DD). Patient-specific IVD finite element (FE) models will be
coupled to agent-based (AB)/network cell models, to predict catabolic shifts of
cell activity in function of morphological, metabolic and mechanical factors.
According to subsequent machine learning analyses, specific combination of
factors will be identified as possible risks for DD.
Low back pain
(LBP) affects up to 85% of people at some point in life. It is strongly related
to DD, with phenotypes that cannot be explained solely by genetic factors as
they also depend on mechanical loads.
In vivo or
in-vitro studies investigated DD at the cell and tissue levels, but they are
costly and limited in terms of parameterization, effective number of
measurements and long-term observations. In contrast, computational modelling
allows testing different boundary conditions (mechanical, biochemical, …) and
numerous theoretical hypotheses over long timescales, at a relatively limited
cost.
Coupled to
personalized organ models, multiscale models and simulations can indicate
common patterns in specific groups of IVD, as well as critical combinations of
cell stimuli and the effects thereof on DD observable features. In particular,
the mining of model inputs together with simulated data can reveal such
patterns and combinations.
The successful
candidate will join the BCN MedTech team and will be co-supervised by
faculties, experts in computational multiscale modelling and machine learning.
(S)He will systematically analyze the 3D anatomy of 500 patient-specific IVD FE
models, available at UPF, to define relevant groups of FE /AB multiscale
simulations. Then, (s)he will use machine learning algorithms to build
correlation models among personalized model inputs and predicted cell activity,
to create a DD risk score model.
D-Risc will
involve key collaborations with population cohort infrastructures in UK and
Finland.
PRINCIPAL INVESTIGATOR
& CONTACT AT HOST
Dr Jérôme Noailly
Contact: jerome.noailly@upf.edu
Barcelona
Centre for New Medical Technologies (BCN MedTech)
Department
of Information and Communication Technologies
Universitat Pompeu Fabra, Barcelona, Spain
ADDITIONAL INFO
Press articles related with the work of the BCN
MedTech BMMB team in disc degeneration:
CONTRACT CONDITIONS &
ELEGIBILITY
The maximum total
payment amount will be €122,592, as broken down below:
- Three annual payments
of €34,800 each one. Where applicable, the amounts corresponding to the Social
Security contributions payable by the employer (in this case, the host
institution), as well as any other compulsory fee, whether current or that may
be provided for in a future legal framework, will be deducted from the yearly
gross amount of €34,800 to be received by the fellow.
- €3,564 per year, as an
additional amount for conferences, courses, research stays, consumables,
equipment, charges for the use of intellectual property, etc. This additional
amount will be managed by the centre for the benefit of the fellow and must be
justified separately.
- ”la Caixa” Banking
Foundation will award a prize of €7,500, which will be paid in the fourth year,
should the fellow be able to deposit their thesis within 6 months after the
third year of their fellowship has ended.
- ”la Caixa” Banking Foundation
will sign an agreement with the host institution, which will receive the
fellowship payment directly. This must be wholly allocated to cover the amounts
arising from Social Security contributions and other required corporate
expenses payable by the employer, where applicable, as well as the fellow’s
gross stipend and the additional amount.
Eligibility:
- Experience: At the call
deadline, applicants must be in the first four years (full-time equivalent
research experience) of their research careers and not yet have been awarded a
doctoral degree.
- Studies pursued: At the
time of recruitment, candidates must comply with one of the following options:
- To have completed the
studies that lead to an official university degree adapted to the European
Higher Education Area awarding 300 ECTS credits, of which at least 60 ECTS
credits must correspond to master level.
- To have completed a
degree in a university not adapted to the European Higher Education Area that
gives access to doctoral studies. The verification of an equivalent level of
studies to the ones mentioned above will be made by the university when the
admission procedure starts.
- Geographic mobility: For
candidates applying to Spanish centres or units: Candidates must not have
resided or have carried out their main activity (work, studies, etc.) in Spain
for more than 12 months in the 3 years immediately prior to the call deadline.
- Level of English:
Candidates must have a demonstrable level of English (B2 or higher).
APPLICATION & DEADLINES
How to apply: https://obrasociallacaixa.org/en/investigacion-y-becas/becas-de-la-caixa/doctorado-inphinit/incoming
Deadline: 4 February 2020
Important dates:
18 February 2020 – Deadline for submitting the
language certificate.
16 April 2020 – Notification of the shortlist
results.
27 and 28 May 2020 – Face-to-face interviews in
Barcelona.
2 June 2020 – Publication of the final list of
selected candidates.
From 2 to 30 June 2020 – Matching research
centre – fellow.
