2,042 research outputs found
Towards in vivo g-ratio mapping using MRI: unifying myelin and diffusion imaging
The g-ratio, quantifying the comparative thickness of the myelin sheath
encasing an axon, is a geometrical invariant that has high functional relevance
because of its importance in determining neuronal conduction velocity. Advances
in MRI data acquisition and signal modelling have put in vivo mapping of the
g-ratio, across the entire white matter, within our reach. This capacity would
greatly increase our knowledge of the nervous system: how it functions, and how
it is impacted by disease. This is the second review on the topic of g-ratio
mapping using MRI. As such, it summarizes the most recent developments in the
field, while also providing methodological background pertinent to aggregate
g-ratio weighted mapping, and discussing pitfalls associated with these
approaches. Using simulations based on recently published data, this review
demonstrates the relevance of the calibration step for three myelin-markers
(macromolecular tissue volume, myelin water fraction, and bound pool fraction).
It highlights the need to estimate both the slope and offset of the
relationship between these MRI-based markers and the true myelin volume
fraction if we are really to achieve the goal of precise, high sensitivity
g-ratio mapping in vivo. Other challenges discussed in this review further
evidence the need for gold standard measurements of human brain tissue from ex
vivo histology. We conclude that the quest to find the most appropriate MRI
biomarkers to enable in vivo g-ratio mapping is ongoing, with the potential of
many novel techniques yet to be investigated.Comment: Will be published as a review article in Journal of Neuroscience
Methods as parf of the Special Issue with Hu Cheng and Vince Calhoun as Guest
Editor
Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational grids
During the last two years the RealityGrid project has allowed us to be one of
the few scientific groups involved in the development of computational grids.
Since smoothly working production grids are not yet available, we have been
able to substantially influence the direction of software development and grid
deployment within the project. In this paper we review our results from large
scale three-dimensional lattice Boltzmann simulations performed over the last
two years. We describe how the proactive use of computational steering and
advanced job migration and visualization techniques enabled us to do our
scientific work more efficiently. The projects reported on in this paper are
studies of complex fluid flows under shear or in porous media, as well as
large-scale parameter searches, and studies of the self-organisation of liquid
cubic mesophases.
Movies are available at
http://www.ica1.uni-stuttgart.de/~jens/pub/05/05-PhilTransReview.htmlComment: 18 pages, 9 figures, 4 movies available, accepted for publication in
Phil. Trans. R. Soc. London Series
Error estimates for solid-state density-functional theory predictions: an overview by means of the ground-state elemental crystals
Predictions of observable properties by density-functional theory
calculations (DFT) are used increasingly often in experimental condensed-matter
physics and materials engineering as data. These predictions are used to
analyze recent measurements, or to plan future experiments. Increasingly more
experimental scientists in these fields therefore face the natural question:
what is the expected error for such an ab initio prediction? Information and
experience about this question is scattered over two decades of literature. The
present review aims to summarize and quantify this implicit knowledge. This
leads to a practical protocol that allows any scientist - experimental or
theoretical - to determine justifiable error estimates for many basic property
predictions, without having to perform additional DFT calculations. A central
role is played by a large and diverse test set of crystalline solids,
containing all ground-state elemental crystals (except most lanthanides). For
several properties of each crystal, the difference between DFT results and
experimental values is assessed. We discuss trends in these deviations and
review explanations suggested in the literature. A prerequisite for such an
error analysis is that different implementations of the same first-principles
formalism provide the same predictions. Therefore, the reproducibility of
predictions across several mainstream methods and codes is discussed too. A
quality factor Delta expresses the spread in predictions from two distinct DFT
implementations by a single number. To compare the PAW method to the highly
accurate APW+lo approach, a code assessment of VASP and GPAW with respect to
WIEN2k yields Delta values of 1.9 and 3.3 meV/atom, respectively. These
differences are an order of magnitude smaller than the typical difference with
experiment, and therefore predictions by APW+lo and PAW are for practical
purposes identical.Comment: 27 pages, 20 figures, supplementary material available (v5 contains
updated supplementary material
Towards in vivo g-ratio mapping using MRI: Unifying myelin and diffusion imaging
BACKGROUND: The g-ratio, quantifying the comparative thickness of the myelin sheath encasing an axon, is a geometrical invariant that has high functional relevance because of its importance in determining neuronal conduction velocity. Advances in MRI data acquisition and signal modelling have put in vivo mapping of the g-ratio, across the entire white matter, within our reach. This capacity would greatly increase our knowledge of the nervous system: how it functions, and how it is impacted by disease. NEW METHOD: This is the second review on the topic of g-ratio mapping using MRI. RESULTS: This review summarizes the most recent developments in the field, while also providing methodological background pertinent to aggregate g-ratio weighted mapping, and discussing pitfalls associated with these approaches. COMPARISON WITH EXISTING METHODS: Using simulations based on recently published data, this review reveals caveats to the state-of-the-art calibration methods that have been used for in vivo g-ratio mapping. It highlights the need to estimate both the slope and offset of the relationship between these MRI-based markers and the true myelin volume fraction if we are really to achieve the goal of precise, high sensitivity g-ratio mapping in vivo. Other challenges discussed in this review further evidence the need for gold standard measurements of human brain tissue from ex vivo histology. CONCLUSIONS: We conclude that the quest to find the most appropriate MRI biomarkers to enable in vivo g-ratio mapping is ongoing, with the full potential of many novel techniques yet to be investigated
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