Quantitative ultrashort TE imaging of the short-T2 components in skeletal muscle using an extended echo-subtraction method.

PURPOSE: To introduce an ultrashort echo time (UTE) based method for quantitative mapping of short-T2 signals in skeletal muscle (SKM) in the presence of fat, with the aim of monitoring SKM fibrosis. METHODS: From a set of at least five UTE images of the same slice, a long- T2* map, a fat-fraction map, and a map of short-T2 -signal fraction are extracted. The method was validated by numerical simulations and in vitro studies on collagen solutions. Finaly, the method was applied to image the short-T2 signals in the leg of eight healthy volunteers. RESULTS: The imaged short-T2 -signal fractions in the collagen solutions correlated with their respective collagen concentrations ( R=0.999,  P=0.009). Short-T2 tissues such as cortical bone and fasciae were highlighted in the resulting short-T2 fraction maps. A significant fraction of short-T2 signal was systematically observed in the skeletal muscle of all of the subjects (4.5±1.2%). CONCLUSION: The proposed method allows the quantitative imaging of short-T2 components in tissues containing fat. By also having the fat-fraction and T2* maps as outcomes, long-T2 suppression is accomplished without requiring modifications to the basic UTE sequence. Although the hypersignal observed in the fasciae suggests that the short-T2 signal observed in SKM might arise from interstitial connective tissue, further investigation is necessary to confirm this statement. Magn Reson Med 78:997-1008, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Restricted diffusion in a model acinar labyrinth by NMR: theoretical and numerical results.

A branched geometrical structure of the mammal lungs is known to be crucial for rapid access of oxygen to blood. But an important pulmonary disease like emphysema results in partial destruction of the alveolar tissue and enlargement of the distal airspaces, which may reduce the total oxygen transfer. This effect has been intensively studied during the last decade by MRI of hyperpolarized gases like helium-3. The relation between geometry and signal attenuation remained obscure due to a lack of realistic geometrical model of the acinar morphology. In this paper, we use Monte Carlo simulations of restricted diffusion in a realistic model acinus to compute the signal attenuation in a diffusion-weighted NMR experiment. We demonstrate that this technique should be sensitive to destruction of the branched structure: partial removal of the interalveolar tissue creates loops in the tree-like acinar architecture that enhance diffusive motion and the consequent signal attenuation. The role of the local geometry and related practical applications are discussed.

A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins.

The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white-beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38,240 RAD-tags and 52,981 nuclear SNPs shared between both species. We have estimated overall higher levels of nucleotide diversity in white-sided (π = 0.0492 ± 0.0006%) than in white-beaked dolphins (π = 0.0300 ± 0.0004%). White-sided dolphins sampled in the Faroe Islands, belonging to two pods (N = 7 and N = 11), showed similar levels of diversity (π = 0.0317 ± 0.0007% and 0.0267 ± 0.0006%, respectively) compared to unrelated individuals of the same species sampled elsewhere (e.g. π = 0.0285 ± 0.0007% for 11 Scottish individuals). No evidence of higher levels of kinship within pods can be derived from our analyses. When identifying the most likely number of genetic clusters among our sample set, we obtained an estimate of two to four clusters, corresponding to both species and possibly, two further clusters within each species. A higher diversity and lower population structuring was encountered in white-sided dolphins from the north-east Atlantic, in line with their preference for pelagic waters, as opposed to white-beaked dolphins that have a more patchy distribution, mainly across continental shelves.

Susceptibility contrast and transverse relaxation in porous media: simulations and experiments.

A numerical simulation of spin diffusion in inhomogeneous magnetic fields due to susceptibility contrast was developed to describe the transverse relaxation of fluids in porous media. The simulation results are in quantitative agreement with experimental measurements obtained on samples of simple geometry. They also confirm the interpretation of the 1H transverse relaxation observed in natural rocks either hydrophilic or hydrophobic for several deuterium oxide/oil saturations, based on the traditional description of water and oil arrangement.

Trabecular bone characterization with low-field MRI.

Multiple-echo (ME) T2 measurements were performed in vitro at 0.1 T on a series of human trabecular bone samples filled with water and compared to site-matched bone density measurements. Multiple-echo T2 is strongly correlated to bone density and allows distinction between samples of equivalent bone density. Multiple-echo T2 is also dependent on the trabecular orientation with respect to the direction of the main field.

NMR diffusion of hyperpolarised 3He in aerogel: a systematic pressure study.

Diffusion of hyperpolarised 3He in a silica aerogel sample with 98% porosity was measured by NMR, and systematically studied as a function of pressure P in the range 20 mbar -1 bar. Spin-echo amplitudes, recorded with pulsed gradients in the usual CMPG sequence, follow a monoexponential decay, and the decay rate varies quadratically with the gradient intensity: thus the apparent diffusion coefficient of the gas D can be evaluated. Our results show a power-law (1/D proportional to P(0.55)), which could be consistent with a fairly broad mean free path distribution, implying some inhomogeneity in the aerogel structure. We have observed a spatial non-uniformity of D, and some deviation to the quadratic dependence of the decay rate with the gradient intensity, possibly related to sample structure inhomogeneity.

Quantitative porosity profiles and wettability contrast visualisation in sandstone by CPMG imaging.

CPMG imaging is applied to the visualisation of porosity and wetting heterogeneities in water saturated sandstone samples at 0.1 T. Porosity profiles from NMR imaging are in agreement within 1% with the standard core analysis. T2 calculated profiles show a factor greater than two between water-wet and oil-wet samples; thus, wettability contrast can be easily visualised.

Comparative measurements between a new logging tool and a reference instrument.

Measurements were performed on reference samples (D2O-H2O mixtures) and on highly heterogeneous rocks (Vosges sandstone) with a new logging tool designed to give access to a high spatial resolution, below 1.5 cm on the vertical scale, for a toroidal sensitive volume of 20 cm3. The results were compared to measurements obtained on a clinical magnetic resonance imaging (MRI) equipment working at the same frequency (4.3 MHz). T2 differences as high as 30% were observed for the reference samples; the shortest values were obtained with the logging tool. Porosity profiles of the rock samples were also compared to reference profiles obtained with a conventional computed tomography (CT) scanner. Both nuclear magnetic resonance (NMR) measurements underevaluate porosity by 2-4% for short T2 values (< 10 ms).

Characterisation of wetting heterogeneities in sandstone rocks by MRI.

MRI is applied to the visualisation of wetting heterogeneities evidenced by water proton T1 contrast at 0.1 T. Water saturated Fontainebleau sandstone samples were examined either in their original water-wet condition, or after silanation. T1, T2Hahn, and T2CPMG were measured for several porosities. T1 and T2CPMG of hydrophobic samples are both twice longer than those of hydrophilic ones. This good contrast allows us to observe wetting heterogeneities in T1-profiles and T1-weighted images.

Bone labelling on micro-magnetic resonance images.

The study of trabecular bone is receiving increasing interest within the medical community working in the field of skeletal diseases, such as osteoporosis. Quantification of trabecular bone structure usually requires as a starting point a correct segmentation of the trabecular network. We have developed a probabilistic relaxation labelling technique, which uses local features of the trabecular bone images to improve segmentation. Tests on synthetic images show that bone labelling performs a more accurate segmentation than conventional techniques such as thresholding, especially by preserving the connectivity of the trabecular network. Tests on acquired data show that porosity values obtained after segmentation are in good agreement with experimental values obtained by weighing the bone samples.

Evaluation of error bounds on calcaneal speed of sound caused by surrounding soft tissue.

For absorptiometry measurements, soft tissue may have an impact on quantitative ultrasound (QUS) measurements. In the present study, we focused primarily on the quantification of measurement error on speed of sound (SOS) caused by surrounding soft tissue. The relevant soft tissue parameters affecting the inherent SOS inaccuracies are thickness and sound velocity. To meet our goal, SOS measurements were taken at the right heel using a QUS imaging device in 21 healthy subjects. Site-matched measurements of soft tissue thickness (STT) and bone width were performed using magnetic resonance imaging of the heel. Several bone velocities were calculated either by accounting for bone width (SOSBW) only or by taking into account the exact path lengths of all major components traversed by ultrasound &lapr;V(b)). Given that soft tissue composition is difficult to determine in vivo, we chose to estimate lower and upper error bounds on bone velocity (V(b lower) and V(b upper)) by spanning the full range of available values in the literature. The mean BW was 30.7 +/- 2.7 mm and the mean medial and external STTs were 8.8 +/- 1.7 and 8.5 +/- 1.5 mm, respectively. Accounting for true BW only resulted in no significant difference between SOS (1533 +/- 37) and SOSBW (1531 +/- 33). By contrast, accounting for both true BW and surrounding soft tissue resulted in an increase in the calculated bone velocity and statistically significant differences between SOS and V(b upper) (1568 +/- 36) and V(b lower) (1542 +/- 34). Root mean square errors between SOS and the calculated velocities were 0.34, 2. 32, and 0.70% for SOSBW, V(b upper), and V(b lower), respectively. We report here measurement errors caused by soft tissue to be 3 to 20 times higher than the SOS short-term precision (SOS coefficient of variation of 0.1%). Our results suggest that inaccuracies in SOS measurement caused by overlying soft tissue cannot be neglected. Overlying soft tissues may influence outcomes of longitudinal studies, especially if variations in tissue thickness and composition occur during the longitudinal follow-up. A practical way of minimizing the measurement error could be to perform an adequate correction for the overlying soft tissue. However, ideally, this should require knowing both the thickness and sound velocity in soft tissue. One might preferably conduct experimental investigations that directly control soft tissue thickness and composition to resolve this problem.

The first proton NMR imaging of ice: stray-field imaging and relaxation studies.

A proton magnetic resonance image of ice was observed with the stray-field (STRAFI) technique. A preliminary study of proton relaxation times was performed in water and ice, at different temperatures. For example, a value of 3.5 micros for the spin-spin relaxation time, T(2), was found in ice at 258 K. Such a short T(2) value leads to significant signal loss, as compared to liquid water, and to a shortening of the STRAFI echo-trains. In particular, a STRAFI signal for protons in ice could be observed only at echo times as short as 15 and 25 micros, for RF pulse durations corresponding to 90 degrees and 50 degrees magnetisation tip angles, respectively. This behaviour is in contrast with that of deuteriated water. Imaging ice, as shown here, opens new prospects in studies involving environmental and materials science, for example.

A network-based analysis of allergen-challenged CD4+ T cells from patients with allergic rhinitis.

We performed a network-based analysis of DNA microarray data from allergen-challenged CD4(+) T cells from patients with seasonal allergic rhinitis. Differentially expressed genes were organized into a functionally annotated network using the Ingenuity Knowledge Database, which is based on manual review of more than 200,000 publications. The main function of this network is the regulation of lymphocyte apoptosis, a role associated with several genes of the tuber necrosis factor superfamily. The expression of TNFRSF4, one of the genes in this family, was found to be 48 times higher in allergen-challenged cells than in diluent-challenged cells. TNFRSF4 is known to inhibit apoptosis and to enhance Th2 proliferation. Examination of a different material of allergen-stimulated peripheral blood mononuclear cells showed a higher number of interleukin-4(+) type 2 CD4(+) T (Th2) cells in patients than in controls (P<0.01), as well as a higher number of non-apoptotic Th2 cells in patients (P<0.01). The number of Th2 cells expressing TNFRSF4, TNFSF7 and TNFRSF1B was also significantly higher in patients. Treatment with anti-TNFSF4 resulted in a significantly decreased number of Th2 cells (P<0.05). A logical inference from all this is that the proliferation of allergen-challenged Th2 cells is associated with a decreased apoptosis of Th2 cells and an increase in TNFRSF4 signalling.