The ISBGroup Blog

The ISBGroup Blog

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

AstraZeneca Award

NewsPosted by Elin Nyman Thu, February 08, 2018 12:19:19

Elin was recently awarded the prestigious AstraZeneca Science Award 2017 in the category Post-Doc. All the short-listed candidates was invited to the ceremoni with dinner at the Guildhall in the centre of the historic city of Cambridge. The top-right picture shows Elin being interviewed directly after the prize ceremony answering the typical question "how does it feel".


NewsPosted by Markus Karlsson Sun, November 19, 2017 17:52:49
In october, I went to Barcelona to attend the annual meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB). Gunnar also came for one day. I presented a poster about my work modelling liver function. I also presented a poster and gave a short "lightning talk" on behalf of Mikael Forsgren, who could not attend.


Karin nailed her thesis

NewsPosted by Karin Lundengård Thu, November 16, 2017 09:38:27
A couple of weeks before defending a thesis, it is common that the PhD student nails their thesis to a log in some of the common areas of the university. This is done to annouce that the student intends to defend their thesis and that anyone who wishes may read it and attend the defense to ask questions. The nailing is then celebrated with delicious cake.

I, Karin Lundengård, have now nailed my thesis ”Mechanistic Modelling - a BOLD Response to the fMRI Information Loss Problem” and I will defend it on the 30:th of November, 13.15 in Hugo Theorells sal (Northern Entrance, Floor 9). My opponent will be Kamil Uludag, Associate Professor at the Faculty of Psychology and Neuroscience at Maastricht University in the Netherlands.

Anyone who wants to attend the defense is welcome.

The full thesis is available at the following link:

English abstract:
Functional Magnetic Resonance Imaging (fMRI) is a common technique for imaging brain activity in humans. However, the fMRI signal stems from local changes in oxygen level rather than from neuronal excitation. The change in oxygen level is referred to as the Blood Oxygen Level Dependent (BOLD) response, and is connected to neuronal excitation and the BOLD response are connected by the neurovascular coupling. The neurons affect the oxygen metabolism, blood volume and blood flow, and this in turn controls the shape of the BOLD response. This interplay is complex, and therefore fMRI analysis often relies on models. However, none of the previously existing models are based on the intracellular mechanisms of the neurovascular coupling. Systems biology is a relatively new field where mechanistic models are used to integrate data from many different parts of a system in order to holistically analyze and predict system properties. This thesis presents a new framework for analysis of fMRI data, based on mechanistic modelling of the neurovascular coupling, using systems biology methods.
Paper I presents the development of the first intracellular signaling model of the neurovascular coupling. Using models, a feed-forward and a feedback hypothesis are tested against each other. The resulting model can mechanistically explain both the initial dip, the main response and the post-peak undershoot of the BOLD response. It is also fitted to estimation data from the visual cortex and validated against variations in frequency and intensity of the stimulus. In Paper II, I present a framework for separating activity from noise by investigating the influence of the astrocytes on the blood vessels via release of vasoactive sub- stances, using observability analysis. This new method can recognize activity in both measured and simulated data, and separate differences in stimulus strength in simulated data. Paper III investigates the effects of the positive allosteric GABA modulator diazepam on working memory in healthy adults. Both positive and negative BOLD was measured during a working memory task, and activation in the cingulate cortex was negatively correlated to the plasma concentration of diazepam. In this area, the BOLD response had decreased below baseline in test subjects with >0.01 mg/L diazepam in the blood. Paper IV expands the model presented in Paper I with a GABA mechanism so that it can describe neuronal inhibition and the negative BOLD response. Sensitization of the GABA receptors by diazepam was added, which enabled the model to explain how changes to the BOLD response described in Paper III could occur without a change in the balance between the GABA and glutamate concentrations.
The framework presented herein may serve as the basis for a new method for identification of both brain activity and useful potential biomarkers for brain diseases and disorders, which will bring us a deeper understanding of the functioning of the human brain.

New Student - Josef

NewsPosted by ISB Group Thu, October 26, 2017 14:51:36

This autumn, we welcome another new student in our group: Josef Grännö

Hello, my name is Josef, I study medicine, and I’m here at ISB Group to do a project for my 6th semester.

My project is about glycemic management in patients admitted to the intensive care unit. During my time here I will compare different models that aim to be used as decision support systems to help ICU staff maintain the patient’s glucose levels in optimal range. I collaborate mainly with the GlucoSafe group that is based in Aarhus, Denmark.

When not desperately trying to understand mathematics I enjoy the outdoors, volleyball and amateur acting.

New student - Christian

NewsPosted by ISB Group Tue, October 17, 2017 13:10:22
This autumn, we welcome another new student in our group: Christian Simonsson


My name is Christian Simonsson and I will be doing my master thesis here in the ISB-group. I am a 5th year engineering biology student with my master’s profile being Materials and Sensors in Biomedince. For my master’s thesis I wanted to do something a bit different from what I have been doing the last two years. Since my Bachelor’s project was on the topic of systems biology, and since I have an interest in modeling (in biology and physiology ), I was very pleased when I was given the opportunity to do my thesis here in the ISB group.

Adiponectin, which is a hormone released by mature adipocyte has been shown to have an important role in the development of type-2 diabetes. However, the precise underlying mechanisms for the production and release of such hormones in adipocytes are not fully understood. Therefore, an ongoing project in the ISB group has been to use mathematical modeling to describe the exocytosis of white adipocytes to predict adiponectin secretion, making it possible to quantify the exocytosis and endocytosis rates. An article on the subject was recently published by William Lövfors et al and in my project I will make use of the model presented in this article. The goal is to extend the model to also describe the experimental data for adiponectin secretion induced through the activation of beta-adrenergic signaling pathways upon extracellular adrenalin stimulation. Hopefully this might contribute to creating a more complete framework for understanding the regulation of this important metabolic hormone.

New student

NewsPosted by ISB Group Tue, October 17, 2017 11:19:21

This autumn, we welcome another new student in our group: Sofie Johansson

Hi! I’m Sofie.

I graduated from medical school spring 2017. A few years ago I did my undergraduate project in another scientific group and subsequently kept working there for a while. I was mainly looking at cardiovascular risk factors among adolescents.

In spite of great supervision I wanted to try another scientific field and have now ended up as a student in the ISB group to work on a project in systems biology. My job at the moment is to build a model of the lactate metabolism in the brain.

New student - Victor

NewsPosted by ISB Group Tue, October 17, 2017 11:01:01

This autumn, we welcome another new student in our group: Victor Viberg

Hi, my name is Victor Viberg. I’m studying biomedical engineering at Linköping University, currently I’m working on my master thesis in the ISB-group at IMT.

The goal of my project is to create a model that can explain the metabolic fluxes of a cancer cell and how it differs from a regular healthy cell. Hopefully this new insight will help in developing more effective treatments for cancer. The model is based on isotropic labeling of metabolites, and it is the first time this type of data is available for a whole human cell. My work will build on the previous work of Nicolas Sundqvist.

New student - Thea

NewsPosted by ISB Group Mon, October 16, 2017 15:41:04
This autumn, we welcome another new student in our group: Thea Sandqvist


My name is Thea and I'm here in the ISB Group to do a project in systems biology for my 6th semester in Medicine.

My project is about insulin- and glucose metabolism in rodents switching between chow- and high fatty based-diets. The project is based on a multi-level-multi-scale model conducted by former ISB Group-member Niclas Berqqvist. My experimental data comes from Karin G. Stenkula and her research group in Lund.

Besides spending time at the office I enjoy an occational pain-au-chocolat (or two or five).

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