The ISBGroup Blog

Nicolas’s master thesis
defence

Last week a member of our group held his master thesis defence. The
member in question was Nicolas who has been doing in his master thesis in our
group, as well as some work prior to that.

Nicolas hold a well-structured and informative presentation of his work
and defended his thesis in a great way.

Nicolas project aimed to characterize the metabolic fluxes of carbon-13
labelled metabolites throughout parts of the metabolic system. The fluxes were
determined from the structure of the metabolites in the end of the metabolic
system. By knowing the reactions in the system and the number of intermediate
products from the inserted labelled metabolites, one can determent the fluxes
between the reactions. This method is called metabolic flux analysis. Although
this is to hard math to do by hand, one can use mathematical modelling.

The second part of Nicolas project was to validate that his model could accurately
predict the quantities of the metabolic fluxes. However, today, there is no
established method for this kind of validation. Nicolas validated his model by the
model’s ability to predict a validation dataset, data that the model have not
seen before. By using this approach, one wish to see how the model react to new
data and judge the model quality by how true the model’s prediction of this
data is.

Additionally, the uncertainty of the predictions was analysed with a
profile likelihood analysis. With such predictions, one can place more trust in
fluxes determined by the model. Consequently, this allows for more challenging
issues to be tackled in the development process of new treatments.

With this we want to congratulate Nicolas on his completed master thesis
and wish good luck in the future.

On November 16th and 17th Gunnar, Elin, William, Tilda, Christian, Kajsa and Jonna attended the 3th national diabetes summit in Stockholm. During
this conference the Karolinska institute was the scene of many interesting conversations,
posters and presentations.

The program consisted of many interesting presentations
covering various aspects of diabetes research. Our group was represented with,
apart from a poster, a very nice talk by Elin. We have had many interesting conversations
with other researchers that may lead to some very nice collaborations. For me
personally the conference was a unique chance to see what kind of diabetes
research is performed in Sweden.

Since the end of November is approaching rapidly my time in
Sweden is almost coming to an end. I look back at a very nice time in Sweden were
I’ve learned a lot about modeling and applications of modeling to the liver.
And of course my new knowledge about things like Fika and warm meals during
lunch 😉

Regards, Jonna

Last week we attended the Ph.D defence of Belén Casas, who has worked with our group during her research.

It was a pleasure to listen to the great presentation of her work and her defence. A short description about her work follows below.

Belén’s work aimed at improving the current diagnostic tools in the field of heart diseases. By analysing data gathered from using 4D flow-MRI (a technique with 3D time resolution and phase contrast magnetic resonance imaging) with mathematical models, Belén has developed tools that can be of help to improve a subject specific assessment of a patient’s cardiovascular function.

After a successful defence, there was a celebratory afterwork in Belén’s honour. We want to take our time to congratulate Belén to her well-deserved Ph.D title and wish her good luck in her future work.

Links to published articles
Briding the gap between measurment and modelling: a cardiovascular functional avatar

Non-invasive Assessment of Systolic and Diastolic Cardiac Function During Rest and Stress Conditions Using an Integrated Image-Modelling Approach

At the time of writing some members of the ISB-group (Henrik, Kajsa and Gunnar) just returned from attending the retreat of the research network CircM. Here they took part of presentations born from the network, one of which Gunnar took part in. Discussions of how the network can move forward with new ideas and challanges were also a part of the agenda.

We enjoyed the retreat, which took place outside Norrköping, and we are glad that we could take part of the presentations and discussions during the retreat.

Down below we leave you a link if you want to check out CircM and get into contact with the network.
https://liu.se/forskning/liu-circm

Regarding the picture down below, the wheater was unaccounted for, and an idea of a picture with Bråviken as background, turned out to be one with a nice forrest background instead.

Last week some of us (Gunnar, William, Christian, Fredrik and Thea) went to Gothenburg to attend the Second Swedish Diabetes Summit. It’s a summit bringing together basic and clinical research.

We had a good time listening to some really interesting presentations with topics varying from treatment of metabolic diseases to artificial intelligence in health and diabetes. Gunnar was chairman for the session of AI and he and William also presented a poster each.

/Thea

As part of the collaboration with ”Forska Utan Djurförsök” (The Swedish Fund for Research without Animal Experiments), ISB group is going to Almedalen in July. Almedalen is the biggest political event of the year in Sweden, and Gunnar Cedersund has been invited to participate in two events:

* Monday July 3, 13-14.30 in Maltfabriken. Then Gunnar and a few others will give short initial presentations, followed by a panel debate with politicians, and ended with some hands-on tutorials, by some of the students from ISBgroup. If you want to try to simulate our own models for diabetes, you should come then. (link to more info)

* Thursday July 6, 10-11.30 in Maltfabriken. Then a short introduction will be followed by a longer session with hands-on testing, not only regarding mathematical models but also regarding other experimental alternatives to animal experiments. The focus then is on chemicals and cosmetics testing (involving e.g. the qsar model). (more info)

Apart from these two events, Forska utan djurförsök will also have a final opportunity to come and talk with them on Friday July 7, at 10-11.30 in Maltfabriken. This will be a more informal event, with the opportunity to come and talk and have coffee with people who know a lot about these issues (link).

Welcome!
Karin for ISBgroup

There is a workshop upcoming about modelling of biological systems at Linköping university. It will take place Thursday-Friday this week, May 11-12, 2017, and is open to everybody who wants to attend: students, scientists, and the general public. We will contribute with one presentation, at Thursday 16-16.20. This presentation will consist of an overview of our modelling philosphy and of our various modelling projects. Apart from us there will be some 20-25 other groups who will present as well. Almost all of the presenters either still work, or have worked, at LiU, i.e. Linköping university.

More information about the workshop can be found here.

Last Friday, one of our Ph.D. students – Mikael Forsgren – nailed up his Ph.D. thesis on our local thesis tree. He thus followed in the footsteps of many many others, ranging back possibly even beyond Martin Luther, by thus publically announcing that he has something that he would like to publically discuss: the thoughts and results in his thesis.

The formal defense will be held at 13.15 in Eken, at HU, Linköping, Sweden. The opponent will be Stephen Sourbron, from Leeds, who is an expert on perfusion modelling in different organs. Mikael’s thesis is about modelling of not only perfusion, but also of intracellular uptake and release, concerning the contrast agent Primovist. He shows how the estimation of such uptake properties using mechanistic modelling can be used to obtain new patient-specific biomarkers, which can be obtained from MRI examinations, and which thus can move to eventually become a non-invasive replacement for today’s invasive liver biopsy examinations. The goal is that this should lead to a reduction in healthcare cost and individual suffering, and to an increase in accuracy and diagnostic power.

Welcome!