Paper quantifying uncertainties of tracer distribution in the brain published in FBCNS

Our paper on “Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields” is now published in Fluids and Barrier of the Central Nervous System. Our main findings are:

  • Uncertainty in diffusion parameters substantially impact the amount of tracer in gray and white matter, and the average tracer concentration in gray and white subregions.
  • Even with an uncertainty in the diffusion coefficient of a factor three, and a resulting fourfold variation in white matter tracer enhancement, discrepancies between simulations of diffusion and experimental data are too large to be attributed to uncertainties in the diffusion coefficient alone.
  • A convective velocity field modelling the glymphatic theory did not increase tracer enhancement in the brain parenchyma compared to pure diffusion. However, when a large-scale directional structure was added to this glymphatic velocity field, tracer inflow increased.
Illustration of velocity field modelling large-scale directionality associated with a glymphatic circulation

Intracranial pressure elevation alters CSF clearance pathways

Our preprint on Intracranial pressure elevation alters CSF clearance pathways is now out on bioRxiv! 

Infusion testing is a common procedure to determine whether shunting will be beneficial in patients with normal pressure hydrocephalus. The method has a well-developed theoretical foundation and corresponding mathematical models that describe the CSF circulation from the choroid plexus to the arachnoid granulations. Here, we investigate to what extent the proposed glymphatic or paravascular pathway (or similar pathways) modifies the results of the traditional mathematical models.

We used a two-compartment model consisting of the subarachnoid space and the paravascular spaces. For the arachnoid granulations, the cribriform plate, capillaries and paravascular spaces, resistances were calculated and used to estimate flow before and during an infusion test. Next, pressure in the subarachnoid space and paravascular spaces were computed. Finally, different variations to the model were tested to evaluate the sensitivity of selected parameters.

At baseline, we found a very small paravascular flow directed into the subarachnoid space, while 60% of the fluid left through the arachnoid granulations and 40% left through the cribriform plate. However, during the infusion, paravascular flow reversed and 25% of the fluid left through these spaces, while 60% went through the arachnoid granulations and only 15% through the cribriform plate.

The relative distribution of CSF flow to different clearance pathways depends on intracranial pressure (ICP), with the arachnoid granulations as the main contributor to outflow. As such, ICP increase is an important factor that should be addressed when determining the pathways of injected substances in the subarachnoid space.

New (old) paper published on automated adjoints of coupled PDE-ODE systems!

Our paper on Automated adjoints of coupled PDE-ODE systems is now published online in the SIAM Journal on Scientific Computing (SISC). Mathematical models that couple partial differential equations (PDEs) and spatially distributed ordinary differential equations (ODEs) arise in biology, medicine, chemistry, and many other fields. In this paper we discuss an extension to the FEniCS finite element software for expressing and efficiently solving such coupled systems. Given an ODE described using an augmentation of the Unified Form Language (UFL) and a discretization described by an arbitrary Butcher tableau, efficient code is automatically generated for the parallel solution of the ODE. The high-level description of the solution algorithm also facilitates the automatic derivation of the adjoint and tangent linearization of coupled PDE-ODE solvers. We demonstrate the capabilities of the approach on examples from cardiac electrophysiology and mitochondrial swelling.

New paper on personalized simulations of cancer treatment published!

Our paper on Towards personalized computer simulation of breast cancer treatment: a multi-scale pharmacokinetic and pharmacodynamic model informed by multi-type patient data has been published online in Cancer Research. (The bioRxiv preprint is also available.) For a popular science account, read about the study in the research magazine Apollon.

cancer-2019-fig1

Abstract: The usefulness of mechanistic models to disentangle complex multi-scale cancer processes such as treatment response has been widely acknowledged. However, a major barrier for multi-scale models to predict treatment outcomes in individual patients lies in their initialization and parametrization which need to reflect individual cancer characteristics accurately. In this study we use multi-type measurements acquired routinely on a single breast tumor, including histopathology, magnetic resonance imaging, and molecular profiling, to personalize parts of a complex multi-scale model of breast cancer treated with chemotherapeutic and anti-angiogenic agents. The model accounts for drug pharmacokinetics and pharmacodynamics. We developed an open-source computer program that simulates cross-sections of tumors under 12-week therapy regimens and use it to individually reproduce and elucidate treatment outcomes of four patients. Two of the tumors did not respond to therapy, and model simulations were used to suggest alternative regimens with improved outcomes dependent on the tumor’s individual characteristics. It was determined that more frequent and lower doses of chemotherapy reduce tumor burden in a low proliferative tumor while lower doses of anti-angiogenic agents improve drug penetration in a poorly perfused tumor. Furthermore, using this model we were able to predict correctly the outcome in another patient after 12 weeks of treatment. In summary, our model bridges multi-type clinical data to shed light on individual treatment outcomes.

What can uncertainty quantification tell us about solute spread in the brain?

Our new preprint on Uncertainty quantification of parenchymal tracer distribution using random diffusion and convective velocity fields is now out on bioRxiv! My first time submitting to bioRxiv rather than good old arXiv.

Over the last decade, there has been a significant renewed interest in the waterscape of the brain; that is, the physiological mechanisms governing cerebrospinal fluid (CSF) and interstitial fluid (ISF) flow in (and around) the brain. A number of new theories have emerged, but a great deal of uncertainty relating to the roles of diffusion, convection and clearance within the brain remains. With this study, we aimed to rigorously quantify how the aforementioned uncertainties in the physiological parameters and in ISF flow affect the spread of a tracer into the brain. We assumed movement of tracer in the brain  to occur by diffusion and/or convection. To account for uncertainty and variability, we circumvented the lack of precise parameter values by modelling velocity and diffusivity as Matérn stochastic fields. We then set up a PDE model with these stochastic (random) fields as coefficients and quantify the uncertainty in the model prediction via the Monte Carlo (MC) method.

 

FEniCS install via Docker

I have finally updated my laptop from the arcane Ubuntu 16.04 to 18.04. First thing to configure: fluxbox :heart: of course. Second, xterm and emacs font, size and color. And third, custom FEniCS installation! Very easy this time around, but recording it here for future reference:

# Install curl 
sudo apt install curl

# Download FEniCS project script
curl -s https://get.fenicsproject.org | bash

# fenicsproject script is installed as /foo/.local/bin/fenicsproject
# Add to e.g. .bashrc:
# export PATH=/foo/.local/bin/fenicsproject:$PATH

# Check that you are using the expected version of fenicsproject, by
# examining output of
which fenicsproject

# Ready to go!
fenicsproject run