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The ISBGroup Blog

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

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

Uncategorised Posted 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 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 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 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 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 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



In News: Say hello to your digital twin

News Posted on Thu, April 21, 2022 07:00:00

An article about the Digital Twin Technology has been published in the latest issue of LiU Magazine.

Säg hej till din digitala tvilling (LIU MAGASIN NUMMER ETT 2022, s16-17)

The online version (In Swedish only) can be found here.



Last day to register: BME@LiU 2022

Events Posted on Thu, April 14, 2022 07:00:00

Today is the last day to register to the Biomedical Engineering conference at Linköping University the 28th of April, BME@LiU 2022.

Don’t miss the chance to see cool examples of combination between technology and medicine. You will be able to meet companies, researchers, and students. Get inspired, learn more about cutting-edge research, and why not discuss new collaborations. The conference will be held at Campus US, but you can also join us online.

For more information about the conference click here.

To register click here.

Contact: bme.at.liu@imt.liu.se



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