Communication

The Disc4All EU ITN project was well represented at the 7th ORS-PSRS 2024 meeting at Skytop, Philadelphia, USA with 2 talks and 3 posters! ESR Sofia Tseranidou won the best poster award with her preject on ¨How to uncover p-p interactions from a regulatory network model through graph neural networks and by using gene ontologies¨. She was even happier to share this with ESR Katherine Crump who won the best posium presentation award! The Disc4All PIs: Prof. Christine Le Maitre, Prof. Jérôme Noailly, Prof Benjamin Gantenbein, Prof. Karin Wuertz-Kozak and ESR Paola Bermudez Lekerika also attended this meeting.

Congratulations again to all the winners!

Disc4All Consortium

We are pleased to inform you that the Disc4All Project has a new Doctor!

We congratulate Dr. SAI NATARAJAN THRISSUR RANGANATHAN, who defended his dissertation on October 29th and obtained the grade of Excellent.

As well, we congratulate his thesis supervisors Dr. Miguel Ángel González Ballester and Dr. Ludovic Humbert (3D Shaper Medical S.L.)

Thesis title: High resolution 3D modelling of lumbar spine from MRI using deep learning Committee: President: Dr. Simo Saarakkala (University of Oulu, Finland)

Secretary: Dr. Federico Sukno (UPF)

Member: Dr. Peter Seevinck (Utrecht University MRIGuidance)

Good luck, Sai! Disc4All Consortium

UPF

At the end of September, Prof. Jérôme Noailly had the great pleasure to present the experience and outcomes of Disc4All EU Project, in a talk about International Collaborations, at the Career Development Session "Establishing International Research Collaborations - Building Connections", of the American Society for Bone and Mineral Research (ASBMR) 2024 Annual Meeting, in Toronto, Canada.

During the last four years, 15 PhD Candidates from 10 different nationalities have spread over 17 institutions and companies of eight different countries, to focus on translational intervertebral disc research and transversal training.

Thanks to the joint scientific work developed in these entities, including: Universitat Pompeu Fabra; University of Oulu; 3D-Shaper Medical; University of Bern; Protavio Ltd; Sheffield Hallam University; The University of Sheffield; University of Liège; KU Leuven; King's College London; Hospital del Mar Research Institute; Barcelona Supercomputing Center; InSilicoTrials; Agència de Qualitat i Avaluació Sanitàries de Catalunya (AQuAS); Rochester Institute of Technology; The University of Hong Kong; Tampere University,

along with a strong international mobility of our researchers, we have achieved great things:

- Building tools for phenotype-based intervertebral disc modelling: Terence McSweeney, Narasimharao Kowlagi, Sai Natarajan, Estefano Muñoz-Moya

- Building hybrid experimental-computational approaches, for integrative biology-based modelling of intervertebral disc cell regulation: Paola Bermudez Lekerika, Andrea Nüesch, Katherine Crump, Exarchos Kanelis, sofia tseranidou, Ahmad Alminnawi

- Building tools for multiscale integration of intervertebral disc biology, omics and disease phenotypes: Roger Compte Boixader, Francesco Gualdi, sofia tseranidou, Estefano Muñoz-Moya, Ahmad Alminnawi, Dimitrios Lialios

- Buiding computational platform for data and hashtag#modelling and simulation tool integrations, in intervertebral disc research: Maria Paola Ferri, Francis Chemorion

- Exploiting phenotypes, hybrid data and multiscale modelling tools for radiology - and biology - based stratification of intervertebral disc degeneration in low back pain: Narasimharao Kowlagi, Estefano Muñoz-Moya

More information about scientific production here: https://lnkd.in/di_68n9j

Model repository: https://spineview.upf.edu/

More to come about the platform!

We hope that our experience can be inspiring for future research; many thanks to Nilsson Holguin & Sabashini Ramchand for the invitation to share at the ASBMR Meeting!

UPF

She said ¨I had such an amazing time attending ESB 2024 in Edinburgh last week to present my PhD research and hear about the latest in biomechanics! Very honored to have received both the ESB Travel Grant and the ESB Youngster Committee Poster Award :) Thank you European Society of Biomechanics for putting together a great conference!!! And of course, a special thanks to my Disc4All EU Project colleagues who have supported me throughout.¨ Congratulation, Katherine!

Andrea Nüesch posted a few days ago ¨It was wonderful to return to Davos for the ARI Orthopaedics Conferences meeting for Orthopaedic Infections. I thoroughly enjoyed hearing about orthopedic infections from various perspectives. A highlight for me was receiving an update on Prof. S Rajasekaran's latest studies on intervertebral disc infections. Thank you for organizing such a great conference and for awarding me the Best Presenter Award. It was a pleasure to present my PhD project Disc4All EU Project. ¨

The Human Digital Twin Barcelona Summer School series is co-organized by BCN MedTech at the Department of Information and Communication Technologies, Universitat Pompeu Fabra (UPF) and by the Barcelona International Summer School (BISS), with the collaboration of the UPF department of Medicine and Life Science. It provides junior engineers, early researchers and medical doctors with an integrative view of state-of-the-art research for in silico medicine, following a complete pipeline from basic science and clinical needs, to model application. The Summer School has the support of the Disc4All European Project, European Society of Biomechanics, of the Spanish Network of Excellence in Biomechanics and CompBioMed. The key methodological and technological concepts are enriched by afternoon hands-on sessions that stand for 15,5 hours of transversal training in in silico medicine technologies during the whole week, under the supervision of expert researchers.

This year, we had the pleasure to welcome 18 international speakers and 80+ attendees (online and offline), from different international institutions and Disc4All Project Members.

The Disc4All consortium’s research on intervertebral disc degeneration generates and utilizes a substantial amount of primary and secondary data. Data reusability, repurposing and heterogenous sources create the need for data curation. This paper outlines the strategies employed to bridge the gap between primary and secondary data sources. This involves the use of infrastructures and platforms with standardized data models and architectures that interface with each other seamlessly at the data storage and management layer and the use of ontologies at the semantic layer. Functionality and technical integration capacity tests are done to validate the technical effectiveness of the data storage and management layer and all testcases successfully pass and a comprehensive taxonomy is defined for the semantic layer. A meta(data) protocol is defined to guide data curation efforts and maturity model that employs a data curator log are enforced to serve as a tool for gauging the level of exchangeability and reusability of data. The outcomes demonstrate viability and reliability of the implemented data management framework to foster data collaboration.

Disc4All Consortium

The fourth Disc4All Winter School was hosted by KU Leuven with Organisation Committee: Prof. Lisbet Geris, Bernard Staumont, Ahmad Alminnawi, Dorina Stanculescu, Luca Emili. During this final edition, we were very pleased to welcome on-site and remotely 6 international speakers, 38+ Disc4all Consortium Members, Early Stage Researchers (ESRs) and external attendees. Detailed agenda and information here: https://insilicotrials.com/disc4all/.

4th Disc4All Winter School was held from February 19th to 23rd 2024 at KU Leuven in Belgium, organised by InSilicoTrials Technologies.

The Disc4all Advanced Training Event was hosted by Prof. Dr. Karin Wuertz-Kozak (RIT) and was held in Canandaigua and Rochester (USA) from December 11th to December 15th, 2023. December 11th and 15th were arrival and departure days, respectively, while scientific and career training sessions took place on December 12th, 13th, and 14th (for more details see below). The event included talks from 13 US-based speakers, as well as two hands-on lab training sessions. We hosted a total of 36 participants, including Disc4all Consortium Members, Disc4all Early Stage Researchers, Speakers, and RIT Students/Faculty.

Karin Wuertz-Kozak (RIT)

Ahmad Alminnawi has participated in the Disc4all Advanced Training Event, which took place from 11 to 15 December 2023 in Rochester, NY, USA.

Dear All, As the in silico medicine community continues to grow, there is a need to follow up on the clinical applications of Computer Modelling and Simulation (CM&S). In 2021 we conducted a first clinical survey to collect feedback from clinicians regarding their knowledge, experience and opinions on the application of CM&S in the clinical practice.

We have now just replicated this initiative releasing a second survey that aims to involve more medical doctors worldwide.

The survey is available at this LINK and we have it in 6 different languages (EN, DE, IT, FR, ES, NL).

We would highly appreciate it if you could distribute the survey to your clinical colleagues. Your contribution can really make the difference in expanding the outreach of this important initiative!

IMPORTANT TO KNOW: Who should contribute: any medical doctors of any specialties; Prerequisites: any clinician can contribute, having experience in computational modelling & simulation is not a requirement; Survey length: between 10 to 15 minutes.

VPHi

Paola Bermudez was awarded with an EORS/ON foundation educational grant (500€) for travelling to EORS meeting in Porto (September 27-29). The grants were awarded to highly motivated and talented young investigators. We are really glad that Paola is one of them! 

Osteoarthritis is the most common degenerative joint disease characterized by the destruction of the hyaline cartilage that covers bone surfaces. From the QUAES chair - Universitat Pompeu Fabra - Barcelona we organised a Scientific Coffee on September 22, 2023 to talk about this pathology, which affects 10% of the general population in Spain. Thanks to: ✔️ Jordi Monfort Faure (Hospital del Mar) ✔️ Jerome Noailly (Universitat Pompeu Fabra - Barcelona) ✔️ Josep Vergés Milano (OAFI, Fundación Internacional de Artrosis) ✔️ Anna Garcia- Elias (Cetir Ascires) In total, 34 people attended from the Valencian Association of People Affected by Arthritis (AVAAR), the Spanish Association with Osteoporosis and Osteoarthritis (AECOSAR), the Valencia Arthritis and Osteoporosis Association and the Association of Family and Community Medicine.

UPF

Francesco Gualdi is the Early Stage Researcher 8 - PhD candidate in the European Project “Disc4All”. He completed his bachelor's degree in Biological Sciences at the University of Ferrara with a thesis focused on the characterization of cells coming from intervertebral disc (IVD). He graduated with honors from the University of Verona in 2021 with an M.Sc. in molecular and medical biotechnology. In parallel to his academic career, he had many working experiences as employee and teacher. His Disc4all Project aims to prioritize genes involved in Lumbar Disc Degeneration and to organize the amount of genetic information related to disc degeneration and its comorbidities to better understand its genetic basis and possibly to identify new biomarkers and therapeutic approaches to the disease.

Maria Paola Ferri is the Early Stage Researcher 3 - PhD candidate in the European Project "Disc4All". She graduated in 2018 in Biotechnologies, from the University of Rome La Sapienza, and in 2021 she obtained the Internation Master degree in Bioinformatics from the Alma Mater University of Bolumn. Her master thesis was focused on the creation of Cloud architectures designed to support and instantiate Bioinformatics applications, curing the portability and the user-friendly access to them. Right now, she is holding a position in the Life Science's Department at the BSC (Barcelona Supercomputing Center). Her role in the Disc4All project would be to extend the implementation of the IDD identification and prediction software in development into a Cloud and HPC environment, so to create in the end a portable and ready-to-use front-end workflow in the LBP (low back pain) investigation, for user and non-experts.

Francis Chemorion is the Early Stage Researcher 1 - PhD candidate in the European Project "Disc4All". He is ensuring collection of data from large data infrastructures, curating it with secondary data from models and simulations to come up with a robust integrated model which will be the basis of a central repository for the project with secured remote access and a comprehensive Data Governance framework. He is passionate about data and its use in powering innovation in research. He designs & develops modern enterprise data architectures by leveraging business intelligence tools, big data tools and creative problem solving. He develops software and systems that enable clients to surface information from their systems and draw insights that drive decision making.

Andrea Nüesch is the Early-Stage Researcher 7 – PhD candidate in the European Project “Disc4all”. Andrea graduated at the Swiss Federal Institute of Technology in Zurich (ETH Zurich) with a bachelor’s degree in Health Sciences and Technology, followed by a master’s degree in 2021 with focus on medical technology. For her master’s thesis, she joined the AO Research Institute Davos, where she was part of the group for Intervertebral Disc Regeneration where she investigated the influence of the secretome of primed mesenchymal stromal cells on Interleukin (IL) -1 stimulated Nucleus Pulposus cells. Currently, Andrea is based in the Biomolecular Sciences Research Centre (BMRC) at the Sheffield Hallam University, United Kingdom. The focus of her research is the experimental exploration of the microbiome in degenerated intervertebral discs.

Congratulations to these education grantees and Paola Bermudez Lekerika! The grants were awarded to highly motivated and talented young investigators to attend the EORS Annual Meeting #EORS2023 in Porto, September 27-29! We look forward to meeting you there soon!

Roger Compte Boixader is the Early Stage Researcher 6 - PhD candidate. He studied a Biotechnology BSc and a Bioengineering MSc at Insitute Quimic de Sarrià (IQS) at Ramon Llull University in Barcelona. He undertook a MSc thesis at Massachusetts Institute of Technology (MIT) in Boston where he developed methodologies to study osteoarthritic knee cartilage function recovery from mechanical stimuli and the administration of medication. He joined Disc4All with the aim to assemble and further improve his skills. He looks forward to contributing to Disc4All by analysing the relationship of the gut microbiome and host genetics with disc degeneration through data driven approaches.

Sai Natarajan is the Early Stage Researcher 5 - Ph.D. candidate in the Disc4All European Project. He graduated in 2019 with a degree in Integrated Masters in Computer Applications from SSSIHL, India. Soon after, he started working as an independent researcher in the areas of image segmentation and generative modeling at Zentralklinik, Germany where he developed tools for understanding shape variations and structural changes in the Lumbar Spine. His current position is based at 3D-Shaper Medical and also at the University of Pompeu Fabra. His main focus of research areas include deep learning-based subject-specific segmentation and 2D-3D reconstruction of shape from single-view images. Reconstruction of the vertebral and disc bodies could lead to the finite element analysis for disc degeneration.

Dimitrios Lialios is the Early Stage Researcher 2 – PhD candidate in the European Project “Disc4All”. He graduated from the Aristotle University of Thessaloniki with a Diploma in Mechanical Engineering and specialization in computational methods in structural analysis. His current position is based in Barcelona Supercomputing Center (BSC). His research revolves around the computational aspects of simulating an Intervertebral Disc (IVD). From the development of a poro-visco-hyperelastic numerical model that can run on Alya, BSC’s finite element solver, to the development of an Agent Based (AB) solver that simulates the expression of proteins related to IVD degeneration and finally, their coupling over simulating a highly accurate in-silico model of the IVD. All the applications are optimized for High Performance Computing (HPC).

Terence McSweeney is the Early Stage Researcher 4 - PhD candidate in the European project "Disc4All". He trained originally as an osteopath at the British College of Osteopathic Medicine and went on to lecture there and at Swansea University. He received a MSc in Pain Management from the University of Edinburgh and a PGCert in Teaching in HE from Swansea University. As an osteopath he has worked in a wide range of clinical settings including the NHS in the UK and private practice in Bahrain. Now he has returned to academia full time as an Early Stage Researcher with Disc4All at the University of Oulu, Finland. His research uses deep learning and multi-omics approaches to tackle the interpretation of imaging data in intervertebral disc degeneration.

Narasimharao (Nash) Kowlagi is the Early Stage Researcher 15 - Ph.D. candidate affiliated to the University of Oulu for the European Project "Disc4all". He has a bachelor's degree in Computer Science & Engineering and a master's degree in Machine Learning and Artificial Intelligence. Before Disc4all, he was working for Accenture (~15 years) providing digital solutions for clients internationally. With the Disc4all project, he is excited to pursue his passion for AI in Healthcare and aims to apply his expertise in computer vision to study various medical image modalities. His primary research involves patient stratification by combining clinical and MRI (Spine) data using deep learning techniques and the need for psychological assessments for the patients having lower back pain (LBP).

Estefano Muñoz Moya is the Early Stage Researcher 14 - PhD candidate in the European Project "Disc4All". He has a degree in Engineering Sciences with a mention in Mechanical Engineering (2017), Civil Engineering (2020), and obtained his Master's degree in Mechanical Engineering (2020) from the University of Santiago de Chile. He has dedicated his previous research to two Chilean projects through experimental tests and numerical simulations. His current research focuses on systematizing multiscale modelling of intervertebral disc regularization during degeneration. Molecular/cell and tissue/organ scale models are locally integrated into areas of interest, thus generating an intelligent atlas of simulated data. This will allow the extraction of simulated and real data altogether and the spatio-temporal evolution of degeneration, characterized by specific hierarchies of risk factors and exploitable clinically.

Sofia Tseranidou is the Early Stage Researcher 13 - PhD candidate in the European Project “Disc4All”. She obtained her Bachelor’s Degree in Applied Mathematics and Physical Sciences in the National Technical University of Athens (NTUA) in 2017, while at the same time completed her internship in the Onassis Cardiac Centre of Athens as an assistant to the department of the CT. In 2020 she received her Master’s Degree in Computational Biomedical Engineering in the Universitat Pompeu Fabra (UPF). Her thesis focused in the mechanobiology of the intervertebral disc cartilage endplate. She is a member of the Department of Information and Communication Technologies (DTIC) in UPF, and the aim of her research is the multiscale modelling of the mechanism that take part during intervertebral disc regulation. She explores the dynamics of the cell activity and how it contributes to the tissue turnover to specific regions of interest, by modelling and simulating bottom-up processes of tissue regulation. The results might help the biomedical field by enhancing patients’ general well-being suffering from low back pain (LBP).

Katherine Crump is the Early Stage Researcher 10 - Ph.D. candidate in the European Project "Disc4All". She received her B.S in biomedical engineering at University of Virginia, and then went on to work at a startup and do research at the Auckland Bioengineering Institute before returning to the University of Virginia for her Masters. In her Masters research, she developed a computational model of long-term muscle degeneration in Duchenne muscular dystrophy. With Disc4All, she is very excited to apply her knowledge to combine computational modeling and tissue engineering to improve understanding of the intervertebral disc. The PhD involves an interaction of in silico modeling and evaluating parameters in vitro in organ culture models, such as glucose and lactate concentration, cell survival, and pro-inflammatory cytokines. These models will be evaluated in 3D cell, tissue, and organ cultures involving mechanical stimulation.

Exarchos Kanelis is the Early Stage Researcher – 11, a PhD candidate in the Project “Disc4all”, which uses Intervertebral disc degeneration as a case study for forming a novel approach on how multifactorial disorders could be addressed. He has a BSc in “Molecular Biology & Genetics” from Democritus University of Thrace and an MSc in “Biotechnology” from the Technical University of Denmark. After his studies, he worked in Oxford - UK for two years gaining experience in assay development for biosensors and DNA/RNA sequencing products. His PhD project will take place in Protatonce, a biotechnology company located in Athens, Greece and is specialised in multiplex assay development & production , biomarker discovery, biomarker performance and compound evaluation. He will be using the Luminex technology for analysing hundreds of intracellular and extracellular proteins in order to identify differences in the proteomic profiles between healthy and LDD cells. He will also use in silico and bioinformatic tools to propose the Cell Signalling Pathways that are activated in LDD and propose mechanism-based biomarkers.

Ahmad Alminnawi is the Early Stage Researcher 12 – Ph.D. candidate in the European Project "Disc4All". Graduated with a B.E. in Mechanical Engineering from the Lebanese American University in Lebanon (2018) and with an M.Sc. in Bioengineering from Osaka University in Japan (2021), Ahmad Alminnawi defines himself as an international person with multidisciplinary knowledge and experience. He is currently working as a researcher within a collaboration between Université de Liège and Katholieke Universiteit Leuven in Belgium on the topic of "In vitro and in silico modeling of cartilage endplate degeneration mechanisms" to unravel the source of the largest cause of morbidity worldwide which is lower back pain.

Paola Bermudez-Lekerika is the Early Stage Researcher 9 - PhD candidate in the European Project "Disc4All". She graduated from the University of Navarra with a Bachelor's Degree in Chemistry (20.17) and Biochemisty (2019). Afterwards, she obtained her Master's Degree in Biomedical Research with a speciality in Regenerative Medicine and Advanced Therapies. Her current position is based in Tissue Engineering for Orthopaedics & Mechanobiology Lab, Department of Biomedical Research (DBMR), University of Bern. Her research focuses on understanding the key catabolic phenotypes involved in Intervertebral Disc Degeneration (IDD) and identifying in silico potential gene variants associated with this disease. Identification of these phenotypes and genetic variants could lead to a better understanding of IDD.

Aneta Toncheva

The Fulbright Commission in Ireland annually awards scholarships to Irish and EU students, scholars and professionals to study, research and lecture across all disciplines in the US. Terence McSweeney is delighted to be amongst the Fulbright Commission Ireland 23/24 awardees! He'll be off to University of California, San Francisco next year! Congratulations and good luck, Terence!

Low back pain is one of the so-called Non-Communicable Diseases (NCD), the relative burden of which has steadily increased worldwide since 1990, according to the World Health Organization. To address this problem, Disc4All provides a new generation of professionals with international mobility equipped with a set of unique capabilities to tackle the prevention and management of highly complex disorders through technology. As the Disc4All project is moving forward days after days, we are extremely happy to inform you that the 3rd Winter School was held in Athens, Greece, hosted by Protavio in “NCSR” – Demokritos. From the 20th to the 24th of February 2023, it combined the internal activities of the Disc4All consortium with a series of workshops about Business strategy, Communication, Personal Development and Business Innovation. The program was as intense as enjoyable. The first days consisted of meetings, presentations, discussions and project assessment by the Project Officer Mr. Thomas Vyzikas. The internal activities were followed by two days of hard work focused on workshops and lectures. Thanks to the great cooperation of international and local experts, all the PhD candidates consolidated their knowledge in a great atmosphere. We are very thankful for the great hospitality and social event of our partners from Greece. We are now very much looking forward to seeing you during the Barcelona 7th VPH Summer School, 5-9 June 2023.

Marta Pulido (IDIBAPS, Universitat de Barcelona)

Christine Le Maitre

Jérôme Noailly

Catedra UPF-QUAES (Spanish version)

Catedra UPF-QUAES (English version)

Liesbet Geris

UPF

UPF

IMIM

UPF

UPF