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Here you can read about everything that's happening in the ISB Group.

Two-hour STRATIF-AI session in ISMH conference

Uncategorised Posted on Thu, May 23, 2024 16:17:07

Two days after STRATIF-AI was featured at the BME@LIU-day in Linköping, Sweden, it is featured again in the ISMH conference in Technirghiol, Rumania. In Linköping, we had a shared booth with SUND (the spin-off company that converts the digital twins to eHealth products), and produced a roll-up and a poster. This roll-up has now been transported to Rumania, together with Gunnar Cedersund, to be displayed at a 2h session at the ISMH conference. This happens today May 23, at 17-19, CET, and can be viewed online.

ISMH stands for the International Society of Medical Hydrology and Climatology. In other words, the conference deals with water-based treatments, such as spas (German: kurort), mineral waters, mud baths, as well as temperature-based treatments, such as saunas, ice-baths, etc. These are old traditional treatments, that dates back to ancient Greek, at the least, but there is also a growing scientific interest, with 10 times more papers published per year today, compared to 20 years ago. Still, the ISMH is old, by scientific standards, and the conference celebrated its 125th birthday yesterday. In the picture below, you see Prof, MD Gelu Onose, one of our main collaborators in STRATIF-AI, and also one of the the main organizer of the event, who cut the first piece of the cake, during yesterday’s celebration.

While the official motto of the conference is “Evidence-based balneology”, while there are lots of medical doctors and professors here, and while balneology is an established speciality in medicine in quite a few countries in Europe, it is still a field that lies on the fringes of medicine. For instance, in Sweden, balneology is not an established discipline of medicine, and MDs cannot become specialized in this field, as they can in e.g. cardiology, or hepatology. Therefore, balneology is to some extent similar to other alternative treatments, such as yoga, regular exercise and gym-based personal trainers, health coaches, etc. They exist in society, they work with health, there is some scientific support for the health benefits of these activities, but they are to a large extent not integrated in conventional healthcare. This is where the activities and visions of STRATIF-AI can contribute. Our ambition is to go from a doctor-centric fragmented system, to an integrated patient-centric eco-system system (see picture below). In this eco-system, e.g. personal trainers can take over where nurses leave a patient, following a health conversation (as in our clinical study 2 in STRATIF-AI). And in this eco-system, one can add new actors, such as spas and kurorts, as long as there is evidence that their methods work, and as long as the underlying mechanisms can be added to the digital twin’s models and visualizations.

The 2h session we will have is structured as follows: First, Gunnar Cedersund, the coordinator of STRATIF-AI gives an overview of STRATIF-AI, and of the digital twins, which converts knowledge and data to computational models. Thereafter Prof Gelu Onose from SCUBA (in the picture above), and his colleagues Constantin Munteanu and Cristina Popescu (both MDs), give an overview of the scientific basis for prevention and treatment of stroke using different modalities, including balneology. Thereafter, we look at the data integration aspects: Jesper Fellenius from Z2 gives an overview of the personal data vault, Cati Martinez from University of Murcia talks about their work with semantic harmonization and inter-operability, and SIMAVI talk about their work on Electronic Healthcare Records, and app developments, e.g. for rehabilitation of stroke. The session is concluded with a round-table discussion. All things can be followed online, at this link. The general link to the conference is available here.



BME@LIU day 2024

Uncategorised Posted on Mon, May 20, 2024 23:42:45

Tomorrow, May 21, 2024, we are arranging a new edition of the BME@LIU-day. BME stands for biomedical engineering, i.e. the interplay between biomedicine (from basic science to clinical practice) and engineering. In practice, BME, entails fields such as modelling and AI, digital twins, wearable sensors, new biomaterials, eHealth, bioinformatics, imaging, bio-optics, etc etc. BME is therefore also one of the core areas of LIU, and it is – in fact – one of the reasons why Linköping university (LIU) was founded, in 1975: to create a bridge between the needs for new engineers at SAAB, and the need for new biomedical research and personnel at the hospital. Around this need, LIU was founded, and at the heart of this dream of a bridge between these two worlds was the Department of Biomedical Engineering (IMT).

IMT eventually attracted Gunnar Cedersund, who started there gradually from around 2011, and then gradually moved his research group over to this department. IMT has since then also expanded its mission to support biomedical engineering beyond its own department, i.e. at the university level. And the arrangement of this BME@LIU-day is a central part of this new broader mission.

In practice, the day will feature a lot of activities at LiU, and also a lot of our own activities. For instance: at 10-10.30, postdoc William Lövfors and MD/Ph.D. student Valentin Kindesjö will introduce the latest developments of our digital twins, using a so-called double presentation where a clinician and an engineer each presents from their specific perspective. In the same session on modelling and AI, at 10.50-11.10, we also see presentations by our newly transitioned postdoc Nicolas Sundqvist, who will present a new story, where we quantify the importance of different cell types for the neurovascular coupling. Finally, also in that session, at 11.20-11.40, we have one of our newest postdocs, Dirk de Weerd, who presents a work he has done together with our incoming postdoc Rasmus Magnusson, on the usage of Variational AutoEncoders, to identify a compressed space for gene expression variations, and apply this to disease modelling. A final oral presentation, not by us, but by one of our closest collaborators, is that 10.50-11.10 by Jesper Fellenius, who will present his perspectives from 20 years of app developments for commercial companies (Ericsson, Swedbank etc) and his 75 MSEK development of a personal data vault. Link to the modelling presentation is here and link to Jesper’s session is here.

Finally, apart from oral presentations, we will also be featured in various places in the poster session combined with the arena. There will be 6 student-based posters, who present 6 large B.Sc. projects, on various modelling tasks within the digital twin development: i) on blood pressure and exercise, ii) on exercise and VO2max, iii) on dysfunctional fat storage in large adipocytes and liver fat, iv) on the neurovascular coupling, v) on drugs and cognitive function, and vi) on alcohol metabolism. Apart from that, there will be many other research-based posters from our group. Finally, we will also – for the first time – be featured not only by our original spin-off company SUND sound medical decisions, but by the newly created daughter company with Z2 and Johan Holmsäter – with the working title Lev Skönare.

All these companies and research projects will be featured with oral presentations, posters, or exhibitions, where you also can test to create your own digital twin, if you want.

Welcome!

Gunnar Cedersund, chair of the program committee



A physiologically-based digital twin for alcohol consumption

Uncategorised Posted on Mon, May 20, 2024 08:16:35

Our work “A physiologically-based digital twin for alcohol consumption—predicting real-life drinking responses and long-term plasma PEth“, has now been published in npj Digital Medicine.

In this manuscript we establish a mathematical model describing short-term alcohol dynamics, with or without simultaneously eating. We then go on to use this short-term model to make predictions about the appearance of the long-term alcohol marker Phosphatidylethanol (PEth). PEth has shown promise in monitoring alcohol consumption and by utilizing modelling the predictive ability of one’s drinking habits could be improved. Further, these predictive capabilities could make PEth-testing feasible in cases of liver diseases, such as MASLD.

You can read the article at: https://www.nature.com/articles/s41746-024-01089-6



A Recap of the Latest STRATIF-AI Meeting

Uncategorised Posted on Thu, May 16, 2024 18:13:12

On April 11-12, we had a new bi-yearly meeting in STRATIF-AI. This meeting was held in beautiful Nottwil, Switzerland, where the Swiss Paraplegic Research center (SPF) is situated.  SPF is responsible for the work with policy and actions toward stakeholders to achieve ultimate clinical implementation, and they were also the hosts of this event.

We have these events every 6 months, and they serve both the purpose of team building and increased understanding of each others’ perspectives and serve to help us focus on the most urgent and timely topics. This time we focused primarily on the design of the 6 clinical studies, which ethical applications were to be submitted at the end of that month. Four of these studies are dedicated to the collection of patient data, aimed at training both the machine learning algorithms and the mechanistic aspects of digital twins. The remaining two studies focus on the real-world testing of eHealth apps within clinical settings. The largest of those will test whether the digital twin improves clinical health conversations, in 300 patients, compared with 300 matched controls.

Overall, the meeting was a success, and we have now passed the planning phase of the project, with requirement specifications and ethical plans, and are now moving into action: into prototype development of the apps, and towards the first pilot studies. 



Lecture on Friday May 17 in the NBIS AI seminar series

Events, News, Systems biology and science Posted on Thu, May 16, 2024 11:25:59

On Friday, Gunnar Cedersund will give a lecture in the NBIS AI seminar series. NBIS is the National Bioinformatics Infrastructure Sweden, which is a core-facility spread out over all universities in Sweden. In other words, at each university in Sweden, there are some local bioinformaticians located, which helps out in projects. NBIS also arranges a seminar series on artificial intelligence (AI), and the next such lecture – on Friday May 17, at 10AM CET – features Gunnar Cedersund. Gunnar will talk about our digital twins, and about how they can be used to integrate a variety of data, both classical bioinformatics multi-omics data and behavioral and imaging data, into a personal data vault, and into a personalized copy of a patients. More information, abstract, and link to the online lecture is available here: https://scilifelab.atlassian.net/wiki/spaces/IJC/pages/2780758082/Meeting+59+2024-05-17



14 March: Cerebrovascular Reactivity Seminar

Uncategorised Posted on Mon, March 11, 2024 15:23:21

Welcome to Gustav Magnusson’s halftime seminar about Cerebrovascular Reactivity

The session will start with presentations from the opponents, followed by the halftime seminar and subsequent discussions.

The event will take place at Wrannesalen, Linköping University, or you can join online via the following link: https://liu-se.zoom.us/j/4294571948

For me information see below:



STRATIF-AI: Digital Twins for Stoke in Brazil

Uncategorised Posted on Wed, March 06, 2024 06:34:13

Our EU project STRATIF-AI (https://stratif-ai.eu/en), in which we develop digital twins for prevention, acute treatment and rehabilitation of stroke, was presented as part of “Clinical applications of computer modeling” at Latin American Summer School for Computational Neuroscience (LASCON) in Sao Paulo Brazil Jan 2024.

Figure shows how modern medicine has been changing and indicates role of modeling in modern (future) clinical practice — part of personalized medicine, data-mining, self-monitoring, omics, surgical planning, medical education, research, screening, etc



Ph.D. defense by Nicolas Sundqvist: Modelling of cerebral metabolism

Uncategorised Posted on Fri, February 23, 2024 08:41:20

A central part of our digital twins, which underlies all apps in the STRATIF-AI project, are the models we have for the brain. So far these models have mostly focused on the neurovascular coupling (NVC). i.e. on the vascular response to neuronal activity. In our latest Ph.D. thesis “Mathematical Modelling of Cerebral Metabolism: From Ion Channels to Metabolic Fluxes”, which was defended by Dr Nicolas Sundqvist last Friday, we have taken these models to a higher level: to also include more detailed cerebral metabolism.

In the first paper, we use MRS data from humans to develop a small model for central metabolism, which is linked to our NVC models. In the second paper, we focus on cell-specific contributions, and show that inter-neurons might be the most dominant cell type in the NVC response; this puts much of the existing fMRI data into question. In the third paper, we present a detailed model for the most metabolically expensive process in neurons: the ion channels. Finally, in the fourth paper, we have developed a method for how to develop even more detailed intracellular flux models, using 13C-labelled media and a new approach to validation of intracellular flux models. 

Opponent was Dr João Duarte from Lund, and the examination committee consisted of Jeanette Hellgren Kotaleski (KTH), Arvind Kumar (KTH), and Katarina Nöh (Jülich Forschungscentrum).

Congratulations PhD Nicolas Sundqvist!



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