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The ISBGroup Blog

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

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:

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. 

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:

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 (, 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!

UX development workshop with visits from Z2 and Region Östergötland (RÖ)

Uncategorised Posted on Tue, February 20, 2024 09:05:40

During Feb 14 and 15, 2024, we at ISBgroup at Linköping University (LIU) had a few visitors, who joined us for an interactive 2-day workshop on UX-design for our stroke Prevention App development. The Prevention app is developed jointly between Linköping University (LiU) and Z2, as part of the STRATIF-AI Horizon-Europe project (, and it is meant for both primary and secondary stroke prevention. Primary prevention will be done in Region Västerbotten and Region Östergötland, and it involves a so-called Health Dialogue. A Health Dialogue is preceded by measurements of traditional risk factors (blood pressure, blood lipids, fasting glucose, etc), which are discussed together with e.g. a specialized nurse or a physiotherapist. Our app will use digital twins to help explain why a person should care about these risk factors, and how they can change their lifestyle (e.g. exercise more, eat less, take certain medications, etc), to improve the risk factors. Based on this information, the patient then sets some goals, to improve their lifestyle, to reduce one or several of the risk factors. These goals are then worked further on together with a coach and dedicated support-group. Also this subsequent coaching-period will be supported by the app, which thus provides a bridge between traditional healthcare actors, and those not normally integrated in healthcare: coaches, personal trainers, support groups. etc.

During the 2 days workshop, we did various role playing exercises, whiteboard and post-it note sketches, which then will be converted to Figma implementations, which then lead to new user tests, etc. From Z2, we have Jesper Fellenius, who has developed the backend for the personal data vault, where the data are stored, and who also has developed a prior prototype for a similar app, which we re-use. From LIU, we have Dr Gunnar Cedersund, Dr Dirk de Weerd, and M.Sc. student Greta Nilsson, who work with the app development. From Region Östergötland (RÖ), we have MD student Johanna Levander and MD specialist Valentin Kindesjö, who represent clinical needs. Apart from these, we also have Johan Holmsäter and Mats Janson, who represent Lev Skönare and coaching and wellbeing partners, who also are connected to STRATIF-AI.

Exceptional Half-Time Seminars: Meet Christian, Tilda, and Nicolas and Dive into Their Intriguing Research

Uncategorised Posted on Mon, May 08, 2023 08:14:00

Christian Simonsson

Titel: Mathematical modelling of diffuse liver disease

Opponents: Jan Boren and Matthias König

Date: 2023-03-01

Abstract: Christian has worked on constructing mathematical models in the context of NAFLD treatment and disease progression. One project has been focusing on creating a minimal mathematical model capable of simulating different dietary interventions, such low carb high fat diet (LCHF), and high fructose (HC) diets. To better understand treatment connection to changes in lipid fluxes. The second project has focused on determining liver function before hepatectomy, which is the only treatment option for HCC and liver metastasis. The two different projects have focused on each end of the NAFLD disease spectra, and the coming project will focus on modelling of non-alcoholic steatohepatitis (NASH)

Tilda Herrgårdh 

Titel: Hybrid modelling for diabetes and stroke prevention

Opponents: Maria Kjellsson, Anna Nordström

Date: 2023-03-02

Abstract: The long-term goal that the thesis will be a part of is to have a tool for prevention of metabolic and cardiovascular diseases, particularly stroke and its common precursor diabetes.  The plan is to use a digital twin and hybrid modelling. A digital twin can be used to make personalized predictions for different scenarios – lifestyle changes, diets, drugs, etc. – that can then be evaluated and compared. These predictions can include the long-term dynamics of different risk factors relevant for cardiovascular disease, such as BMI or fasting plasma glucose, or short term dynamics such as meal response glucose. These predictions can for example be used to understand the dynamics behind disease progression and to get continuous updated on progress of the changes made in real life, which can hopefully increase medical pedagogics and motivation. The long-term predictions of risk factors can be used in a hybrid modelling scheme as input in a machine learning model to get your risk score for having a stroke within a certain time span. The thesis covers the first steps towards, and a first example of the idea described above, as well as the development of models describing some of the different mechanisms relevant to diabetes and stroke progressions that can later be used in a comprehensive model of the entire progression. 

Nicolas Sundqvist

Titel: Systems modelling of human metabolism: Methods for 13C metabolic flux analysis and applications to the brain

Opponents: Elizabeth Klint, Dr. Katharina Nöh, Dr. Joao Duart

Date: 2023-01-17

Abstract: Nicolas has worked on constructing a mathematical model that can explain the mechanism that regulate the metabolism in the brain. This mathematical model explains what the cerebral metabolic response looks like in response neuronal activity induced by a visual stimulus. Furthermore, the work also includes how these mechanisms for the metabolic response connect to the mechanisms that of the neurovascular coupling. This work has resulted in a manuscript recently accepted for publication and will formed a base for future modelling endeavours. Additionally, Nicolas has worked with modelling intracellular metabolic fluxes using measurements of 13C isotope labels. A lot of this work have gone into method development for modelling stoichiometric models for 13C metabolic flux analysis (MFA) and has resulted in a publication where we present a method for validating such models when there is an uncertainty with respect to experimental measurement uncertainty. The plan for the continued work of Nicolas’ doctoral studies is to apply the methodologies for 13C MFA to a system for studying neurodegenerative diseases in neurological cell lines. As well as to investigate the mechanisms of the regulation of oxygen metabolism with respect to activity in different types of neuronal cells. 

CompBioMed Conference 2023: Munich, 12-14 September

Uncategorised Posted on Tue, April 11, 2023 08:58:00

CompBioMed Conference 2023 (CBMC23) will address all aspects of computational biomedicine, from genome through organ to whole human and population levels, embracing data driven, mechanistic modelling and simulation, machine learning and combinations thereof. This year Gunnar will is one of the Plenary Speakers and he will discuss physiologically based digital twins: a digital and interactive copy of yourself that follows you throughout your health journey.

You can read more about it HERE

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