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

ICSB 2022

Uncategorised Posted by ISB GroupPosted on Mon, October 10, 2022 09:59:46

The 21st International Conference on Systems Biology (ICSB 2022) was held in Berlin, Germany, these past few days. We had a great time there and had the opportunity to meet great people, take part in interesting discussions, and see some of Berlin. During the conference, we presented several posters and gave some talks (summarized below). We would like to extend our thanks to the ICSB committee for a well-organized conference. Until next time, from the ISB group.

The full program can be found here: https://www.icsb2022.berlin/, and down below is a summary of our contributions.

M4-health: digital twins that follow you throughout your health journey, Gunnar Cedersund

Authors: Gunnar Cedersund

An interconnected multi-level mechanistic model of the human brain, Nicolas Sundqvist

Authors: Nicolas Sundqvist, Henrik Podéus, Malin Ejneby Silverå, Sebastian Sten, Salvador Dura-Bernal, Soroush Safaei, Maria Engström and Gunnar Cedersund

Digital twins and hybrid modelling for simulation of physiological variables and stroke risk, Tilda Herrgårdh

Authors: Tilda Herrgårdh, Elizabeth Hunter, Kajsa Tunedal, John D. Kelleher and Gunnar Cedersund

Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling, Kajsa Tunedal

Authors: Kajsa Tunedal, Carl-Johan Carlhäll, Federica Viola, Tino Ebbers and Gunnar Cedersund

Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation, Niloofar Nikaein

Authors: Niloofar Nikaein, Kedeye Tuerxun, Daniel Eklund, Alexander Persson, Robert Kruse, Eva Särndahl, Eewa Nånberg, Antje Thonig, Gunnar Cedersund, Elin Nyman, Dirk Repsilber and On Behalf Of The X-Hide Consortium

Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach, Henrik Podéus

Authors: Henrik Podéus, Gunnar Cedersund and Salvador Dura-Bernal

An in silico resection to estimate global and regional hepatobiliary function in patients undergoing hepatectomy, Christian Simonsson

Authors: Christian Simonsson, Wolf Claus Bartholomä, Anna Lindhoff Larsson, Markus Karlsson, Bengt Norén, Gunnar Cedersund, Nils Dahlström, Per Sandström and Peter Lundberg

A comprehensive mechanistic model of adipocyte signaling with layers of confidence, William Lövfors

Authors: William Lövfors, Cecilia Jönsson, Charlotta S. Olofsson, Gunnar Cedersund and Elin Nyman



Best poster prize at International Study Group for Systems Biology (ISGSB) 2022 conference

Uncategorised Posted by ISB GroupPosted on Tue, October 04, 2022 11:55:23

We recently attended the International Study Group for Systems Biology (ISGSB) 2022 conference where we gave two talks. Our first talk was given by Gunnar Cedersund and was on how we can use M4-models and digital twin tools to help patients on their health journey throughout various aspects of their lives. The second talk was given by Nicolas Sundqvist and was on our efforts to develop an interconnected multi-level mechanistic model of the human brain. The conference was a success as we partook in interesting discussions and offered our contributions to the ISGSB community. On another fun note, our poster designed and presented by Nicolas Sundqvist was voted joint best poster of the conference. We are looking forward to the next iteration of the ISGSB conference.



New Article: Digital twin predicting diet response before and after long-term fasting

Uncategorised Posted by ISB GroupPosted on Mon, September 26, 2022 14:30:55

Read our new article published in PLoS Computational Biology!

You find the full link here:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010469

Silfvergren O, Simonsson C, Ekstedt M, Lundberg P, Gennemark P, Cedersund G. Digital twin predicting diet response before and after long-term fasting. PLoS Comput Biol. 2022 Sep 12;18(9):e1010469. doi: 10.1371/journal.pcbi.1010469.

ABSTRACT

“Fasting and diet are central components of prevention against cardiovascular disease. Unfortunately, there is little consensus regarding which diet schemes are optimal. This is partially because different clinical studies contribute with different non-connected pieces of knowledge, which have not been fully integrated into a useful and interconnected big picture. In principle, mathematical models describing meal responses could be used for such an integration. However, today’s models still lack critical mechanisms, such as protein metabolism and a dynamic glycogen regulation. Herein, we present a) a new expanded model structure including these mechanisms; b) a set of parameters which can simultaneously describe a wide array of complementary estimation data, in both healthy and diabetic populations; c) a personalisation-script, which allows these generic parameters to be tuned to an individual/sub-population, using demographics (age, weight, height, diabetes status) and historic metabolic data. We exemplify how this personalisation can be used to predict new independent data, including a new clinical study, where a qualitatively new prediction is validated: that an oral protein tolerance test gives a clear response in plasma glucose, after, but not before, a 48h fasting period. Our combined model, parameters, and fitting script lay the foundation for an offline digital twin.”



A multi-data based quantitative model for the neurovascular coupling in the brain

Uncategorised Posted by ISB GroupPosted on Thu, September 08, 2022 20:06:18

A while back we made our expanded brain model, capable of describing and predicting various multi-species data, available on bioRxiv (https://doi.org/10.1101/2021.03.25.437053). After some further work we are aiming to submit our work, In the meanwhile feel free to take part of the currently available version.

Abstract: The neurovascular coupling (NVC) forms the foundation for functional imaging techniques of the brain, since NVC connects neural activity with observable hemodynamic changes. Many aspects of the NVC have been studied both experimentally and with mathematical models: various combinations of blood volume and flow, electrical activity, oxygen saturation measures, blood oxygenation level-dependent (BOLD) response, and optogenetics have been measured and modeled in rodents, primates, or humans. We now present a first inter-connected mathematical model that describes all such data types simultaneously. The model can predict independent validation data not used for training. Using simulations, we show for example how complex bimodal behaviors appear upon stimulation. These simulations thus demonstrate how our new quantitative model, incorporating most of the core aspects of the NVC, can be used to mechanistically explain each of its constituent datasets.

Overview of the presented study: A: Cellular pathways underlying the neurovascular coupling (NVC). B. Overview of commonly used experimental techniques C. Overview of the study D. Comparison of different published models describing the NVC with regards to different mechanisms


VPH 2022 – Less than 2 weeks to the conference! 6-9 September, Porto, Portugal  

Uncategorised Posted by ISB GroupPosted on Thu, August 25, 2022 16:41:59

Dont miss the chance to meet us at The Virtual Physiologiacl Human Conference 2022!

We have three presentations and our digital twin will be a part of the welcome reception

Dancing Digital Twins performance

Welcome reception, 7th September, 19:30 Auditorium

Unique collaboration between the Swedish researcher and pianist Gunnar Cedersund and choreographer and dancer Julia Bengtsson fuses digital twin technology and visualization with dance and music

Nicolas Sundqvist

Presentation, 8th September

Session 14: Multiscale modelling. 8.30-10.30, Room 2

An interconnected multi-level mechanistic model of the human brain

Oscar Arrestam

Presentation, 9th September

Session 22: Computational modeling in health and disease 4. 8.45-10.15 Room 2

Digital twin predicting diet response before and after long-term fasting (see poster below)

Gunnar Cedersund

Presentation, 9th September

Session 25: Computational tools and simulation in biomechanics 4

10.30-12.30 Auditorium

M4-health: digital twins that follow you throughout your health journey



The IEE Engineering in Medicine and Biology Conference (EMBC)

Events Posted by ISB GroupPosted on Mon, August 22, 2022 07:00:00

In the middle of July, Kajsa Tunedal went to Glasgow to attend the IEE Engineering in Medicine and Biology Conference (EMBC) (https://embc.embs.org/2022/) and presented an ePoster: “Insights of Hemodynamic Changes in Hypertension and Diabetes through a 4D Flow MRI-Based Personalized Cardiovascular Model”. It was a great experience starting with a very scottish opening ceremony and followed by many interesting talks, workshops, and meetings with other modellers and researchers with interests in cardiovascular mechanisms and measurements.

Kajsa Tundedal showing her poster at the IEE Engineering in Medicine and Biology Conference
Opening cermony at the EMBC conference


New article in PLoS Computational Biology

News, Systems biology and science Posted by ISB GroupPosted on Mon, May 02, 2022 07:00:00

Sundqvist N, Grankvist N, Watrous J, Mohit J, Nilsson R, Cedersund G. Validation-based model selection for 13C metabolic flux analysis with uncertain measurement errors. PLoS Comput Biol. 2022 Apr 11;18(4):e1009999. doi: 10.1371/journal.pcbi.1009999

Author summary: Measuring metabolic reaction fluxes in living cells is difficult, yet important. The gold standard is to label extracellular metabolites with 13C, to use mass spectrometry to find out where the 13C-atoms ends up, and finally use mathematical modelling to calculate how quickly each reaction must have flowed, for the 13C-atoms to end up like that. This measurement thus relies on usage of the right mathematical model, which must be selected among various candidate models. In this manuscript, we present a new way to do this model selection step, utilizing validation data. Using an adopted approach to calculate the uncertainty of model predictions, we identify new validation experiments, which are neither too similar, nor too dissimilar, compared to the previous training data. The model candidate that is best at predicting this new validation data is the one chosen. Tests on simulated data where the true model is known, shows that the validation-based method is robust when the magnitude of the error in the measurement uncertainty is unknown, something that conventional methods are not. This improvement is important since true uncertainties can be difficult to estimate for these data. Finally, we demonstrate how the new method can be used on real data, to identify fluxes and important reactions.



Dancing Digital Twins – Seeing the music of Chopin and and Beethoven

Events Posted by ISB GroupPosted on Wed, April 27, 2022 23:00:44

After many years of preparations – 20+ years of developing the digital twins in general, and now 3-4 years of making them dance – the first lecture-performance is at last about to take place. On Thursday at 17.00 it happens! In this highly innovative event, you will not only be able to see with your eyes what happens in some of the best music ever written, but also be able to see inside a computer copy of some people in the audience – into their digital twins. By looking at and inside these digital twins, we will together explore what happens both in the body when you dance, and in the music that your twins are dancing to.

Does it sound intriguing?

Then come to Berzeliussalen at Linköping University, Campus US, on April 28, at 17-17.45. Welcome!

Read more about the event here



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