Add more brain stuff and new datasets page

Author: finsberg

.cspell_dict.txt

@@ -23,22 +23,26 @@ DOLFINx
 elastodynamics
 electrodiffusive
 Empagliflozin
+endfeet
 ffian
 finsberg
 Finsberg
 Forsch
 Fouilloux
 geometriesx
 Gjerde
+gliovascular
 glymphatic
 gotranx
 Graphnics
 Haubner
+herlyng
 howpublished
 htmlcov
 idealised
 importlib
 Ingeborg
+insilico
 Jørgen
 jorgensd
 Jupyterbook
@@ -66,7 +70,9 @@ odeigah
 oneline
 orcid
 peaceiris
+periarterial
 perivascular
+perivenous
 postprocess
 poulain
 Pycodestyle
@@ -75,15 +81,19 @@ pypi
 pyproject
 pytest
 Ragan
+Ratbrain
+riseth
 saetra
 Sætra
 scientificcomputing
 scifem
+silico
 Simcardems
 Simula
 Stankelbein
 SVMTK
 Valnes
 venv
+vinje
 zapf
 Zenodo

docs/datasets.md

@@ -0,0 +1,28 @@
+# Datasets
+
+This page contains a list of relevant datasets for Scientific Computing.
+
+## Brain MRI and Meshes
+
+- **[Gonzo Dataset](https://zenodo.org/records/14266867)**
+  Human Brain MRI Data of CSF Tracer Evolution Over 72h For Data-Integrated Simulations.
+
+- **[Ratbrain mesh](https://zenodo.org/records/8138343)**
+  Mesh files for rat brain simulations.
+
+- **[MRI2FEM data set](https://zenodo.org/records/4899120)**
+  Data set supporting the MRI2FEM book and workflows.
+
+## Solute Transport and Mechanics
+
+- **[Human brain solute transport meshes](https://zenodo.org/records/8036492)**
+  Example meshes for 'Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation'.
+
+- **[Perivascular space meshes](https://zenodo.org/records/4629927)**
+  Mesh files for idealized and image-based periarterial and perivenous spaces.
+
+- **[Mechanisms behind PVS flow](https://zenodo.org/records/3890133)**
+  Data related to mechanisms behind flow in perivascular spaces.
+
+- **[Geometrically reduced PVS flow](https://zenodo.org/records/5729458)**
+  Data for geometrically reduced modelling of pulsatile flow.

docs/myst.yml

@@ -21,6 +21,7 @@ project:
       children:
         - file: repositories.md
         - file: packages.md
+        - file: datasets.md
     - title: Guidelines for papers with code
       children:
         - file: papers-with-code.md

docs/references.bib

@@ -52,6 +52,23 @@ @article{causemann2022
   publisher     = {Cold Spring Harbor Laboratory},
   journal       = {bioRxiv}
 }
+@article{causemann2025insilico,
+  title         = {In-silico molecular enrichment and clearance of the human intracranial space},
+  author        = {Causemann, Marius and Kuchta, Miroslav and Masri, Rami and Rognes, Marie E.},
+  journal       = {bioRxiv},
+  year          = {2025},
+  doi           = {10.1101/2025.01.30.635680},
+  url           = {https://doi.org/10.1101/2025.01.30.635680}
+}
+@article{causemann2025stretch,
+  title         = {Stretch and flow at the gliovascular interface: high-fidelity modelling of the mechanics of astrocyte endfeet},
+  author        = {Causemann, Marius and Enger, Rune and Rognes, Marie E},
+  journal       = {bioRxiv},
+  pages         = {2025--05},
+  year          = {2025},
+  publisher     = {Cold Spring Harbor Laboratory},
+  doi           = {10.1101/2025.05.08.652799}
+}
 @article{daversin2022,
   author        = {Daversin-Catty, C\'{e}cile and Gjerde, Ingeborg G. and Rognes, Marie E.},
   title         = {{Geometrically Reduced Modelling of Pulsatile Flow in Perivascular Networks}},
@@ -116,6 +133,17 @@ @article{haubner2023
   year          = {2023},
   doi           = {10.1137/21M143114X}
 }
+@article{herlyng2025advection,
+  title         = {Advection versus diffusion in brain ventricular transport},
+  author        = {Herlyng, Halvor and Ellingsrud, Ada J and Kuchta, Miroslav and Jeong, Inyoung and Rognes, Marie E and Jurisch-Yaksi, Nathalie},
+  journal       = {Fluids and Barriers of the CNS},
+  volume        = {22},
+  number        = {1},
+  pages         = {82},
+  year          = {2025},
+  publisher     = {Springer},
+  doi           = {10.1186/s12987-025-00692-3}
+}
 @article{https://doi.org/10.1002/cnm.2982,
   author        = {Finsberg, Henrik and Xi, Ce and Tan, Ju Le and Zhong, Liang and Genet, Martin and Sundnes, Joakim and Lee, Lik Chuan and Wall, Samuel T.},
   title         = {Efficient estimation of personalized biventricular mechanical function employing gradient-based optimization},
@@ -194,6 +222,17 @@ @article{odeigah2024computational
   year          = {2024},
   publisher     = {Frontiers Media SA}
 }
+@article{piersanti2023,
+  title         = {Are brain displacements and pressures within the parenchyma induced by surface pressure differences? A computational modelling study},
+  author        = {Piersanti, Eleonora and Rognes, Marie E. and Vinje, Vegard},
+  journal       = {PLOS ONE},
+  volume        = {18},
+  number        = {5},
+  pages         = {e0288668},
+  year          = {2023},
+  publisher     = {Public Library of Science},
+  doi           = {10.1371/journal.pone.0288668}
+}
 @unpublished{poulain2022,
   title         = {{Multi-compartmental model of glymphatic clearance of solutes in brain tissue}},
   author        = {Poulain, Alexandre and Riseth, J{{\o}}rgen and Vinje, Vegard},
@@ -205,6 +244,15 @@ @unpublished{poulain2022
   hal_id        = {hal-03789563},
   hal_version   = {v1}
 }
+@article{riseth2025human,
+  title         = {Human brain MRI data of CSF tracer evolution over 72h for data-integrated simulations},
+  author        = {Riseth, J{\o}rgen N and Koch, Timo and Lian, Sofie Lysholm and Stor{\aa}s, Tryggve Holck and Zikatanov, Ludmil T and Valnes, Lars Magnus and Nordengen, Kaja and Mardal, Kent-Andr{\'e}},
+  journal       = {medRxiv},
+  pages         = {2025--07},
+  year          = {2025},
+  publisher     = {Cold Spring Harbor Laboratory Press},
+  doi           = {10.1101/2025.07.23.25331971}
+}
 @article{saetra2021,
   doi           = {10.1371/journal.pcbi.1008143},
   author        = {S\ae{}tra, Marte J. AND Einevoll, Gaute T. AND Halnes, Geir},
@@ -254,6 +302,17 @@ @inbook{valnes2022
   isbn          = {978-3-030-95136-8},
   doi           = {10.1007/978-3-030-95136-8_3}
 }
+@article{vinje2023human,
+  title         = {Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation},
+  author        = {Vinje, Vegard and Zapf, Bastian and Ringstad, Geir and Eide, Per Kristian and Rognes, Marie E and Mardal, Kent-Andre},
+  journal       = {Fluids and Barriers of the CNS},
+  volume        = {20},
+  number        = {1},
+  pages         = {62},
+  year          = {2023},
+  publisher     = {Springer},
+  doi           = {10.1186/s12987-023-00459-8}
+}
 @misc{zapf2023medical,
   title         = {Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization},
   author        = {Bastian Zapf and Johannes Haubner and Lukas Baumg\"{a}rtner and Stephan Schmidt},

docs/repositories.md

@@ -2,20 +2,24 @@
 A list of repositories used in research in the Scientific Computing Department follows. A link to relevant publications/preprints is referenced.
 
 ## 2025
+- [In-silico molecular enrichment and clearance of the human intracranial space](https://github.com/MariusCausemann/brain-PVS-SAS-transport) {cite}`causemann2025insilico`
+- [Advection versus diffusion in brain ventricular transport](https://github.com/hherlyng/zebrafish-cilia-csf) {cite}`herlyng2025advection`
+- [Stretch and flow at the gliovascular interface: high-fidelity modelling of the mechanics of astrocyte endfeet](https://github.com/MariusCausemann/endfoot-mechanics) {cite}`causemann2025stretch`
 - [Impact of segregation scheme on performance of a strongly coupled cardiac electromechanical solver](https://github.com/ComputationalPhysiology/simcardems2) {cite}`MYKLEBUST2025118270`
 - [A software benchmark for cardiac elastodynamics](https://github.com/finsberg/cardiac_benchmark) {cite}`arostica2025117485`
 - [Arrhythmic Mitral Valve Syndrome: Insights from Left Ventricular End-Systolic Shape Analysis](https://github.com/ComputationalPhysiology/MAD-SSA) {cite}`monopoli2025arrhythmic`
 - [DeepValve: an automatic detection pipeline for the mitral valve in cardiac magnetic resonance imaging](https://github.com/giuliamonopoli/deepvalve-paper) {cite}`monopoli2025deepvalve`
 
 ## 2024
+- [Human brain MRI data of CSF tracer evolution over 72h for data-integrated simulations](https://github.com/jorgenriseth/gonzo) {cite}`riseth2025human`
 - [The sodium/glucose cotransporter 2 inhibitor Empagliflozin inhibits long QT 3 late sodium currents in a mutation specific manner](https://github.com/andygedwards/LQT3-SGLT2i) {cite}`LUNSONGA202599`
 - [An electrodiffusive network model with multicompartmental neurons and synaptic connections](https://github.com/martejulie/electrodiffusive-network-model) {cite}`saetra2024`
 - [Automatic motion estimation with applications to hiPSC-CMs](https://github.com/ComputationalPhysiology/automatic-motion-estimation) {cite}`10.1088/2057-1976/ad7268`
 - [A computational study of right ventricular mechanics in a rat model of pulmonary arterial hypertension](https://github.com/oscarodeigah/rv_pah_project) {cite}`odeigah2024computational`
 
 
 ## 2023
-
+- [Human brain solute transport quantified by glymphatic MRI-informed biophysics during sleep and sleep deprivation](https://github.com/bzapf/braintransport) {cite}`vinje2023human`
 - [Medical image registration using optimal control of a linear hyperbolic transport equation with a DG discretization](https://github.com/JohannesHaubner/mapMRI) {cite}`zapf2023medical`
 - [ffian: Fluid Flow In Astrocyte Networks](https://github.com/martejulie/fluid-flow-in-astrocyte-networks) {cite}`sætra2023`
 - [A novel density based approach for topology optimization of Stokes flow](https://github.com/JohannesHaubner/TopOpt) {cite}`haubner2023`