Pulsed wave Doppler ultrasound: Accuracy, variability, and impact of acquisition parameters on flow measurements.

BACKGROUND: Pulsed wave Doppler ultrasound is a useful modality for assessing vascular health as it quantifies blood flow characteristics. To facilitate accurate diagnosis, accuracy and consistency of this modality should be assessed through Doppler quality assurance (QA). PURPOSE: The purpose of this study was to characterize the accuracy, reproducibility, and inter-scanner variability of ultrasound flow velocity measurements via a flow phantom, with a focus on the effect of systematic acquisition parameters on measured flow velocity accuracy. METHODS: Using a manufacturer-calibrated flow phantom, pulsed wave measurements were acquired on five clinical systems (iU22, Philips) with three models of transducers, including both linear and curvilinear models. The peak and mean flow velocities were estimated by vendor-supplied spectral analysis tools. To investigate intra- and inter-scanner variability, measurements were repeated using each scanner-transducer pair under a standardized set of conditions. Inter-scanner variability was assessed using ANOVA. Flow velocity accuracy was investigated by mean absolute percentage error. The impacts of receive gain, measurement depth, and beam steering on measured flow velocity accuracy were examined by varying each parameter over its available range and comparing to the ground truth flow velocity. RESULTS: Inter-scanner variability was statistically significant for peak flow measurements made using both linear and curvilinear transducers, though absolute differences in measured velocity were small. Inter-scanner variability was not statistically significant for mean flow velocity. Receive gain, measurement depth, and beam steering were all found to impact the accuracy of measured flow characteristics for linear transducers. Accuracy of the flow measurements made with the curvilinear transducer demonstrated high consistency to changes in receive gain at a constant depth, though were impacted by increasing the measurement depth. CONCLUSIONS: Carefully and consistently selected acquisition and set-up parameters are essential in order to establish a reliable and meaningful QA program.

Optimization of non-endorectal prostate MR image quality using PI-QUAL: A multidisciplinary team approach.

PURPOSE: To evaluate the utility of the PI-QUAL score in assessing protocol changes aimed to improve image quality from a non-endorectal coil prostate MR imaging protocol during a 9-month quality improvement (QI) project and to quantify the inter-reader agreement of PI-QUAL scores between radiologists, technologists, and physicists. METHODS: This retrospective study audited 1,012 multiparametric prostate MRI examinations as part of a national QI project according to the PI-QUAL standard. PI-QUAL scores were used to inform MR protocol changes. Following the project, 4 radiologists, 2 technologists, and 1 medical physicist collectively audited an additional set of 150 examinations to identify statistical improvements in image quality using the two-tailed Wilcoxon rank sum test. The improvements due to individual protocol changes were assessed among subsets of the 1,012 examinations which compared examinations occurring before and after the isolated protocol change. Inter-reader variability was assessed using the percent majority agreement and the average standard deviation of PI-QUAL scores between evaluators. RESULTS: During this QI project, PI-QUAL scores improved from 3.67 ± 0.75 to 4.16 ± 0.59 (p < 0.01) after implementing a series of protocol changes. Among a subset of 451 cases, we found that adopting R/L rather than A/P phase encoding reduced distortion in diffusion-weighted imaging (DW) from 21.6% (41/190 A/P phase encoded cases) to 11.5% (30/261 R/L phase encoded cases) (p < 0.01). Similarly, in the same 451 cases, adopting R/L phase encoding in T2WI reduced breathing motion artifacts from 34.6% (94/272 A/P phase encoding cases) to 12.8% (23/179 R/L phase encoding cases) (p < 0.01). DWI wraparound artifact was mitigated by employing a full-pelvis shim and enabling the abdomen shim option. The occurrence of low signal-to-noise ratio was reduced from 19.4% (19/98 cases without a weight-based threshold) to 6.3% (10/160) by instituting a weight-based threshold for using an endorectal coil (p < 0.01). The percent majority agreement was similar between radiologists, technologists and physicists, and all evaluators combined (72%, 77%, and 67%, respectively). CONCLUSIONS: PI-QUAL can evaluate image quality changes resulting from protocol optimizations at both the exam- and series-levels. With training, radiologists, technologists, and physicists can perform PI-QUAL scoring with similar performance. Broadening the scope of the quality improvement team can result in meaningful and lasting change.

Contrast-Enhanced In-Phase Dixon Sequence: Impact on Biopsy Clip Detection on Breast MRI.

BACKGROUND. Identification of breast biopsy clips using conventional MRI sequences may be challenging. A contrast-enhanced in-phase Dixon sequence may have greater conspicuity for areas of susceptibility compared with standard clinical sequences. OBJECTIVE. The purpose of this article is to compare detection of breast biopsy clips on MRI between the contrast-enhanced in-phase Dixon sequence and three routine clinical sequences. METHODS. This retrospective study included 164 patients (mean age, 50.3 years) with a total of 281 breast biopsy clips who underwent contrast-enhanced breast MRI between January 2, 2019, and April 16, 2020. Three radiologists, blinded to the clip location and sequence used, independently annotated biopsy clip locations on three clinical sequences (T1-weighted non-fat-suppressed [NFS], STIR, and first phase from dynamic contrast-enhanced T1-weighted fat-suppressed [FS]) and on a contrast-enhanced in-phase Dixon sequence and then recorded confidence scores (1-4 scale). A study coordinator used all available imaging and reports to localize clips on MRI, which served as the reference standard. A physicist measured clip CNR. Sequences were compared using the McNemar test and two-tailed Wilcoxon signed rank tests. RESULTS. Among the three readers, pooled sensitivity and PPV were 78.2% and 96.2% for T1-weighted NFS, 26.6% and 92.7% for STIR, 61.7% and 95.9% for contrast-enhanced T1-weighted FS, and 85.1% and 95.1% for contrast-enhanced in-phase Dixon sequence. Pooled sensitivity was higher for contrast-enhanced in-phase Dixon sequence than for the other sequences (all p < .05); pooled PPV was not significantly different between contrast-enhanced in-phase Dixon and the other sequences (all p > .05). Mean confidence scores (pooled across readers for true-positive assessments) and mean CNR were 3.0 ± 0.9 (SD) and 1.21 ± 0.61 for T1-weighted NFS, 1.7 ± 0.9 and 0.57 ± 0.69 for STIR, 2.5 ± 1.0 and 0.54 ± 0.61 for contrast-enhanced T1-weighted FS, and 3.5 ± 0.8 and 4.05 ± 2.6 for the contrast-enhanced in-phase Dixon sequence. Pooled mean confidence scores and CNR were higher for contrast-enhanced in-phase Dixon than for the other sequences (all p < .001). CONCLUSION. Compared with clinical sequences, the contrast-enhanced in-phase Dixon sequence had higher sensitivity for detecting breast biopsy clips on MRI and higher reader confidence and CNR, without change in PPV. CLINICAL IMPACT. The contrast-enhanced in-phase Dixon sequence may help address a current challenge in clinical breast MRI interpretation.

Optimizing Diffusion Imaging Protocols for Structural Connectomics in Mouse Models of Neurological Conditions.

Network approaches provide sensitive biomarkers for neurological conditions, such as Alzheimer's disease (AD). Mouse models can help advance our understanding of underlying pathologies, by dissecting vulnerable circuits. While the mouse brain contains less white matter compared to the human brain, axonal diameters compare relatively well (e.g., ~0.6 µm in the mouse and ~0.65-1.05 µm in the human corpus callosum). This makes the mouse an attractive test bed for novel diffusion models and imaging protocols. Remaining questions on the accuracy and uncertainty of connectomes have prompted us to evaluate diffusion imaging protocols with various spatial and angular resolutions. We have derived structural connectomes by extracting gradient subsets from a high-spatial, high-angular resolution diffusion acquisition (120 directions, 43-µm-size voxels). We have simulated protocols with 12, 15, 20, 30, 45, 60, 80, 100, and 120 angles and at 43, 86, or 172-µm voxel sizes. The rotational stability of these schemes increased with angular resolution. The minimum condition number was achieved for 120 directions, followed by 60 and 45 directions. The percentage of voxels containing one dyad was exceeded by those with two dyads after 45 directions, and for the highest spatial resolution protocols. For the 86- or 172-µm resolutions, these ratios converged toward 55% for one and 39% for two dyads, respectively, with <7% from voxels with three dyads. Tractography errors, estimated through dyad dispersion, decreased most with angular resolution. Spatial resolution effects became noticeable at 172 µm. Smaller tracts, e.g., the fornix, were affected more than larger ones, e.g., the fimbria. We observed an inflection point for 45 directions, and an asymptotic behavior after 60 directions, corresponding to similar projection density maps. Spatially downsampling to 86 µm, while maintaining the angular resolution, achieved a subgraph similarity of 96% relative to the reference. Using 60 directions with 86- or 172-µm voxels resulted in 94% similarity. Node similarity metrics indicated that major white matter tracts were more robust to downsampling relative to cortical regions. Our study provides guidelines for new protocols in mouse models of neurological conditions, so as to achieve similar connectomes, while increasing efficiency.

Mapping and correcting hyperpolarized magnetization decay with radial keyhole imaging.

PURPOSE: Hyperpolarized (HP) media enable biomedical imaging applications that cannot be achieved with conventional MRI contrast agents. Unfortunately, quantifying HP images is challenging, because relaxation and radio-frequency pulsing generate spatially varying signal decay during acquisition. We demonstrate that, by combining center-out k-space sampling with postacquisition keyhole reconstruction, voxel-by-voxel maps of regional HP magnetization decay can be generated with no additional data collection. THEORY AND METHODS: Digital phantom, HP 129 Xe phantom, and in vivo 129 Xe human (N = 4 healthy; N = 2 with cystic fibrosis) imaging was performed using radial sampling. Datasets were reconstructed using a postacquisition keyhole approach in which 2 temporally resolved images were created and used to generate maps of regional magnetization decay following a simple analytical model. RESULTS: Mean, keyhole-derived decay terms showed excellent agreement with the decay used in simulations (R2 = 0.996) and with global attenuation terms in HP 129 Xe phantom imaging (R2 > 0.97). Mean regional decay from in vivo imaging agreed well with global decay values and displayed spatial heterogeneity that matched expected variations in flip angle and oxygen partial pressure. Moreover, these maps could be used to correct variable signal decay across the image volume. CONCLUSIONS: We have demonstrated that center-out trajectories combined with keyhole reconstruction can be used to map regional HP signal decay and to quantitatively correct images. This approach may be used to improve the accuracy of quantitative measures obtained from hyperpolarized media. Although validated with gaseous HP 129 Xe in this work, this technique can be generalized to any hyperpolarized agent.

Multireader Determination of Clinically Significant Obstruction Using Hyperpolarized 129Xe-Ventilation MRI.

OBJECTIVE: The objective of our study was to identify the magnitude and distribution of ventilation defect scores (VDSs) derived from hyperpolarized (HP) 129Xe-MRI associated with clinically relevant airway obstruction. MATERIALS AND METHODS: From 2012 to 2015, 76 subjects underwent HP 129Xe-MRI (48 healthy volunteers [mean age ± SD, 54 ± 17 years]; 20 patients with asthma [mean age, 44 ± 20 years]; eight patients with chronic obstructive pulmonary disease [mean age, 67 ± 5 years]). All subjects underwent spirometry 1 day before MRI to establish the presence of airway obstruction (forced expiratory volume in 1 second-to-forced vital capacity ratio [FEV1/FVC] < 70%). Five blinded readers assessed the degree of ventilation impairment and assigned a VDS (range, 0-100%). Interreader agreement was assessed using the Fleiss kappa statistic. Using FEV1/FVC as the reference standard, the optimum VDS threshold for the detection of airway obstruction was estimated using ROC curve analysis with 10-fold cross-validation. RESULTS: Compared with the VDSs in healthy subjects, VDSs in patients with airway obstruction were significantly higher (p < 0.0001) and significantly correlated with disease severity (r = 0.66, p < 0.0001). Ventilation defects in subjects with airway obstruction did not show a location-specific pattern (p = 0.158); however, defects in healthy control subjects were more prevalent in the upper lungs (p = 0.014). ROC curve analysis yielded an optimal threshold of 12.4% ± 6.1% (mean ± SD) for clinically significant VDS. Interreader agreement for 129Xe-MRI was substantial (κ = 0.71). CONCLUSION: This multireader study of a diverse cohort of patients and control subjects suggests a 129Xe-ventilation MRI VDS of 12.4% or greater represents clinically significant obstruction.

A protocol for quantifying cardiogenic oscillations in dynamic 129 Xe gas exchange spectroscopy: The effects of idiopathic pulmonary fibrosis.

The spectral parameters of hyperpolarized 129 Xe exchanging between airspaces, interstitial barrier, and red blood cells (RBCs) are sensitive to pulmonary pathophysiology. This study sought to evaluate whether the dynamics of 129 Xe spectroscopy provide additional insight, with particular focus on quantifying cardiogenic oscillations in the RBC resonance. 129 Xe spectra were dynamically acquired in eight healthy volunteers and nine subjects with idiopathic pulmonary fibrosis (IPF). 129 Xe FIDs were collected every 20 ms (TE  = 0.932 ms, 512 points, dwell time = 32 µs, flip angle ≈ 20°) during a 16 s breathing maneuver. The FIDs were pre-processed using the spectral improvement by Fourier thresholding technique (SIFT) and fit in the time domain to determine the airspace, interstitial barrier, and RBC spectral parameters. The RBC and gas resonances were fit to a Lorentzian lineshape, while the barrier was fit to a Voigt lineshape to account for its greater structural heterogeneity. For each complex resonance the amplitude, chemical shift, linewidth(s), and phase were calculated. The time-averaged spectra confirmed that the RBC to barrier amplitude ratio (RBC:barrier ratio) and RBC chemical shift are both reduced in IPF subjects. Their temporal dynamics showed that all three 129 Xe resonances are affected by the breathing maneuver. Most notably, several RBC spectral parameters exhibited prominent oscillations at the cardiac frequency, and their peak-to-peak variation differed between IPF subjects and healthy volunteers. In the IPF cohort, oscillations were more prominent in the RBC amplitude (16.8 ± 5.2 versus 9.7 ± 2.9%; P = 0.008), chemical shift (0.43 ± 0.33 versus 0.083 ± 0.05 ppm; P < 0.001), and phase (7.7 ± 5.6 versus 1.4 ± 0.8°; P < 0.001). Dynamic 129 Xe spectroscopy is a simple and sensitive tool that probes the temporal variability of gas exchange and may prove useful in discerning the underlying causes of its impairment.

A portable ventilator with integrated physiologic monitoring for hyperpolarized 129Xe MRI in rodents.

Hyperpolarized (HP) 129Xe MRI is emerging as a powerful, non-invasive method to image lung function and is beginning to find clinical application across a range of conditions. As clinical implementation progresses, it becomes important to translate back to well-defined animal models, where novel disease signatures can be characterized longitudinally and validated against histology. To date, preclinical 129Xe MRI has been limited to only a few sites worldwide with 2D imaging that is not generally sufficient to fully capture the heterogeneity of lung disease. To address these limitations and facilitate broader dissemination, we report on a compact and portable HP gas ventilator that integrates all the gas-delivery and physiologic monitoring capabilities required for high-resolution 3D hyperpolarized 129Xe imaging. This ventilator is MR- and HP-gas compatible, driven by inexpensive microcontrollers and open source code, and allows for precise control of the tidal volume and breathing cycle in perorally intubated mice and rats. We use the system to demonstrate data acquisition over multiple breath-holds, during which lung motion is suspended to enable high-resolution 3D imaging of gas-phase and dissolved-phase 129Xe in the lungs. We demonstrate the portability and versatility of the ventilator by imaging a mouse model of lung cancer longitudinally at 2 Tesla, and a healthy rat at 7 Tesla. We also report the detection of subtle spectroscopic fluctuations in phase with the heart rate, superimposed onto larger variations stemming from the respiratory cycle. This ventilator was developed to facilitate duplication and gain broad adoption to accelerate preclinical 129Xe MRI research.

Using hyperpolarized 129Xe MRI to quantify regional gas transfer in idiopathic pulmonary fibrosis.

BACKGROUND: Assessing functional impairment, therapeutic response and disease progression in patients with idiopathic pulmonary fibrosis (IPF) continues to be challenging. Hyperpolarized 129Xe MRI can address this gap through its unique capability to image gas transfer three-dimensionally from airspaces to interstitial barrier tissues to red blood cells (RBCs). This must be validated by testing the degree to which it correlates with pulmonary function tests (PFTs) and CT scores, and its spatial distribution reflects known physiology and patterns of disease. METHODS: 13 healthy individuals (33.6±15.7 years) and 12 patients with IPF (66.0±6.4 years) underwent 129Xe MRI to generate three-dimensional quantitative maps depicting the 129Xe ventilation distribution, its uptake in interstitial barrier tissues and its transfer to RBCs. For each map, mean values were correlated with PFTs and CT fibrosis scores, and their patterns were tested for the ability to depict functional gravitational gradients in healthy lung and to detect the known basal and peripheral predominance of disease in IPF. RESULTS: 129Xe MRI depicted functional impairment in patients with IPF, whose mean barrier uptake increased by 188% compared with the healthy reference population. 129Xe MRI metrics correlated poorly and insignificantly with CT fibrosis scores but strongly with PFTs. Barrier uptake and RBC transfer both correlated significantly with diffusing capacity of the lungs for carbon monoxide (r=-0.75, p<0.01 and r=0.72, p<0.01), while their ratio (RBC/barrier) correlated most strongly (r=0.94, p<0.01). RBC transfer exhibited significant anterior-posterior gravitational gradients in healthy volunteers, but not in IPF, where it was significantly impaired in the basal (p=0.02) and subpleural (p<0.01) lung. CONCLUSIONS: Hyperpolarized129Xe MRI is a rapid and well-tolerated exam that provides region-specific quantification of interstitial barrier thickness and RBC transfer efficiency. With further development, it could become a robust tool for measuring disease progression and therapeutic response in patients with IPF, sensitively and non-invasively.

Uncovering a third dissolved-phase 129 Xe resonance in the human lung: Quantifying spectroscopic features in healthy subjects and patients with idiopathic pulmonary fibrosis.

PURPOSE: The purpose of this work was to accurately characterize the spectral properties of hyperpolarized 129 Xe in patients with idiopathic pulmonary fibrosis (IPF) compared to healthy volunteers. METHODS: Subjects underwent hyperpolarized 129 Xe breath-hold spectroscopy, during which 38 dissolved-phase free induction decays (FIDs) were acquired after reaching steady state (echo time/repetition time = 0.875/50 ms; bandwidth = 8.06 kHz; flip angle≈22 °). FIDs were averaged and then decomposed into multiple spectral components using time-domain curve fitting. The resulting amplitudes, frequencies, line widths, and starting phases of each component were compared among groups using a Mann-Whitney-Wilcoxon U test. RESULTS: Three dissolved-phase resonances, consisting of red blood cells (RBCs) and two barrier compartments, were consistently identified in all subjects. In subjects with IPF relative to healthy volunteers, the RBC frequency was 0.70 parts per million (ppm) more negative (P = 0.05), the chemical shift of barrier 2 was 0.6 ppm more negative (P = 0.009), the line widths of both barrier peaks were ∼2 ppm narrower (P < 0.001), and the starting phase of barrier 1 was 20.3 ° higher (P = 0.01). Moreover, the ratio RBC:barriers was reduced by 52.9% in IPF (P < 0.001). CONCLUSIONS: The accurate decomposition of 129 Xe spectra not only has merit for developing a global metric of pulmonary function, but also provides necessary insights to optimize phase-sensitive methods for imaging 129 Xe gas transfer. Magn Reson Med 78:1306-1315, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Establishing an accurate gas phase reference frequency to quantify 129 Xe chemical shifts in vivo.

PURPOSE: 129 Xe interacts with biological media to exhibit chemical shifts exceeding 200 ppm that report on physiology and pathology. Extracting this functional information requires shifts to be measured precisely. Historically, shifts have been reported relative to the gas-phase resonance originating from pulmonary airspaces. However, this frequency is not fixed-it is affected by bulk magnetic susceptibility, as well as Xe-N2 , Xe-Xe, and Xe-O2 interactions. In this study, we addressed this by introducing a robust method to determine the 0 ppm 129 Xe reference from in vivo data. METHODS: Respiratory-gated hyperpolarized 129 Xe spectra from the gas- and dissolved-phases were acquired in four mice at 2T from multiple axial slices within the thoracic cavity. Complex spectra were then fitted in the time domain to identify peaks. RESULTS: Gas-phase 129 Xe exhibited two distinct resonances corresponding to 129 Xe in conducting airways (varying from -0.6 ± 0.2 to 1.3 ± 0.3 ppm) and alveoli (relatively stable, at -2.2 ± 0.1 ppm). Dissolved-phase 129 Xe exhibited five reproducible resonances in the thorax at 198.4 ± 0.4, 195.5 ± 0.4, 193.9 ± 0.2, 191.3 ± 0.2, and 190.7 ± 0.3 ppm. CONCLUSION: The alveolar 129 Xe resonance exhibits a stable frequency across all mice. Therefore, it can provide a reliable in vivo reference frequency by which to characterize other spectroscopic shifts. Magn Reson Med 77:1438-1445, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Single-breath clinical imaging of hyperpolarized (129)Xe in the airspaces, barrier, and red blood cells using an interleaved 3D radial 1-point Dixon acquisition.

PURPOSE: We sought to develop and test a clinically feasible 1-point Dixon, three-dimensional (3D) radial acquisition strategy to create isotropic 3D MR images of (129)Xe in the airspaces, barrier, and red blood cells (RBCs) in a single breath. The approach was evaluated in healthy volunteers and subjects with idiopathic pulmonary fibrosis (IPF). METHODS: A calibration scan determined the echo time at which (129)Xe in RBCs and barrier were 90° out of phase. At this TE, interleaved dissolved and gas-phase images were acquired using a 3D radial acquisition and were reconstructed separately using the NUFFT algorithm. The dissolved-phase image was phase-shifted to cast RBC and barrier signal into the real and imaginary channels such that the image-derived RBC:barrier ratio matched that from spectroscopy. The RBC and barrier images were further corrected for regional field inhomogeneity using a phase map created from the gas-phase (129)Xe image. RESULTS: Healthy volunteers exhibited largely uniform (129)Xe-barrier and (129)Xe-RBC images. By contrast, (129)Xe-RBC images in IPF subjects exhibited significant signal voids. These voids correlated qualitatively with regions of fibrosis visible on CT. CONCLUSIONS: This study illustrates the feasibility of acquiring single-breath, 3D isotropic images of (129)Xe in the airspaces, barrier, and RBCs using a 1-point Dixon 3D radial acquisition.

Dose and pulse sequence considerations for hyperpolarized (129)Xe ventilation MRI.

PURPOSE: The aim of this study was to evaluate the effect of hyperpolarized (129)Xe dose on image signal-to-noise ratio (SNR) and ventilation defect conspicuity on both multi-slice gradient echo and isotropic 3D-radially acquired ventilation MRI. MATERIALS AND METHODS: Ten non-smoking older subjects (ages 60.8±7.9years) underwent hyperpolarized (HP) (129)Xe ventilation MRI using both GRE and 3D-radial acquisitions, each tested using a 71ml (high) and 24ml (low) dose equivalent (DE) of fully polarized, fully enriched (129)Xe. For all images SNR and ventilation defect percentage (VDP) were calculated. RESULTS: Normalized SNR (SNRn), obtained by dividing SNR by voxel volume and dose was higher for high-DE GRE acquisitions (SNRn=1.9±0.8ml(-2)) than low-DE GRE scans (SNRn=0.8±0.2ml(-2)). Radially acquired images exhibited a more consistent, albeit lower SNRn (High-DE: SNRn=0.5±0.1ml(-2), low-DE: SNRn=0.5±0.2ml(-2)). VDP was indistinguishable across all scans. CONCLUSIONS: These results suggest that images acquired using the high-DE GRE sequence provided the highest SNRn, which was in agreement with previous reports in the literature. 3D-radial images had lower SNRn, but have advantages for visual display, monitoring magnetization dynamics, and visualizing physiological gradients. By evaluating normalized SNR in the context of dose-equivalent formalism, it should be possible to predict (129)Xe dose requirements and quantify the benefits of more efficient transmit/receive coils, field strengths, and pulse sequences.

Extending semiautomatic ventilation defect analysis for hyperpolarized (129)Xe ventilation MRI.

RATIONALE AND OBJECTIVES: Clinical deployment of hyperpolarized (129)Xe magnetic resonance imaging requires accurate quantification and visualization of the ventilation defect percentage (VDP). Here, we improve the robustness of our previous semiautomated analysis method to reduce operator dependence, correct for B1 inhomogeneity and vascular structures, and extend the analysis to display multiple intensity clusters. MATERIALS AND METHODS: Two segmentation methods were compared-a seeded region-growing method, previously validated by expert reader scoring, and a new linear-binning method that corrects the effects of bias field and vascular structures. The new method removes nearly all operator interventions by rescaling the (129)Xe magnetic resonance images to the 99th percentile of the cumulative distribution and applying fixed thresholds to classify (129)Xe voxels into four clusters: defect, low, medium, and high intensity. The methods were applied to 24 subjects including patients with chronic obstructive pulmonary disease (n = 8), age-matched controls (n = 8), and healthy normal subjects (n = 8). RESULTS: Linear-binning enabled a faster and more reproducible workflow and permitted analysis of an additional 0.25 ± 0.18 L of lung volume by accounting for vasculature. Like region-growing, linear-binning VDP correlated strongly with reader scoring (R(2) = 0.93, P < .0001), but with less systematic bias. Moreover, linear-binning maps clearly depict regions of low and high intensity that may prove useful for phenotyping subjects with chronic obstructive pulmonary disease. CONCLUSIONS: Corrected linear-binning provides a robust means to quantify (129)Xe ventilation images yielding VDP values that are indistinguishable from expert reader scores, while exploiting the entire dynamic range to depict multiple image clusters.

3D MRI of impaired hyperpolarized 129Xe uptake in a rat model of pulmonary fibrosis.

A variety of pulmonary pathologies, in particular interstitial lung diseases, are characterized by thickening of the pulmonary blood-gas barrier, and this thickening results in reduced gas exchange. Such diffusive impairment is challenging to quantify spatially, because the distributions of the metabolically relevant gases (CO2 and O2) cannot be detected directly within the lungs. Hyperpolarized (HP) (129)Xe is a promising surrogate for these metabolic gases, because MR spectroscopy and imaging allow gaseous alveolar (129)Xe to be detected separately from (129)Xe dissolved in the red blood cells (RBCs) and the adjacent tissues, which comprise blood plasma and lung interstitium. Because (129)Xe reaches the RBCs by diffusing across the same barrier tissues (blood plasma and interstitium) as O2, barrier thickening will delay (129)Xe transit and, thus, reduce RBC-specific (129)Xe MR signal. Here we have exploited these properties to generate 3D, MR images of (129)Xe uptake by the RBCs in two groups of rats. In the experimental group, unilateral fibrotic injury was generated prior to imaging by instilling bleomycin into one lung. In the control group, a unilateral sham instillation of saline was performed. Uptake of (129)Xe by the RBCs, quantified as the fraction of RBC signal relative to total dissolved (129)Xe signal, was significantly reduced (P = 0.03) in the injured lungs of bleomycin-treated animals. In contrast, no significant difference (P = 0.56) was observed between the saline-treated and untreated lungs of control animals. Together, these results indicate that 3D MRI of HP (129)Xe dissolved in the pulmonary tissues can provide useful biomarkers of impaired diffusive gas exchange resulting from fibrotic thickening.

Probing the regional distribution of pulmonary gas exchange through single-breath gas- and dissolved-phase 129Xe MR imaging.

Although some central aspects of pulmonary function (ventilation and perfusion) are known to be heterogeneous, the distribution of diffusive gas exchange remains poorly characterized. A solution is offered by hyperpolarized 129Xe magnetic resonance (MR) imaging, because this gas can be separately detected in the lung's air spaces and dissolved in its tissues. Early dissolved-phase 129Xe images exhibited intensity gradients that favored the dependent lung. To quantitatively corroborate this finding, we developed an interleaved, three-dimensional radial sequence to image the gaseous and dissolved 129Xe distributions in the same breath. These images were normalized and divided to calculate "129Xe gas-transfer" maps. We hypothesized that, for healthy volunteers, 129Xe gas-transfer maps would retain the previously observed posture-dependent gradients. This was tested in nine subjects: when the subjects were supine, 129Xe gas transfer exhibited a posterior-anterior gradient of -2.00 ± 0.74%/cm; when the subjects were prone, the gradient reversed to 1.94 ± 1.14%/cm (P < 0.001). The 129Xe gas-transfer maps also exhibited significant heterogeneity, as measured by the coefficient of variation, that correlated with subject total lung capacity (r = 0.77, P = 0.015). Gas-transfer intensity varied nonmonotonically with slice position and increased in slices proximal to the main pulmonary arteries. Despite substantial heterogeneity, the mean gas transfer for all subjects was 1.00 ± 0.01 while supine and 1.01 ± 0.01 while prone (P = 0.25), indicating good "matching" between gas- and dissolved-phase distributions. This study demonstrates that single-breath gas- and dissolved-phase 129Xe MR imaging yields 129Xe gas-transfer maps that are sensitive to altered gas exchange caused by differences in lung inflation and posture.

Multiscale computational analysis of Xenopus laevis morphogenesis reveals key insights of systems-level behavior.

BACKGROUND: Tissue morphogenesis is a complex process whereby tissue structures self-assemble by the aggregate behaviors of independently acting cells responding to both intracellular and extracellular cues in their environment. During embryonic development, morphogenesis is particularly important for organizing cells into tissues, and although key regulatory events of this process are well studied in isolation, a number of important systems-level questions remain unanswered. This is due, in part, to a lack of integrative tools that enable the coupling of biological phenomena across spatial and temporal scales. Here, we present a new computational framework that integrates intracellular signaling information with multi-cell behaviors in the context of a spatially heterogeneous tissue environment. RESULTS: We have developed a computational simulation of mesendoderm migration in the Xenopus laevis explant model, which is a well studied biological model of tissue morphogenesis that recapitulates many features of this process during development in humans. The simulation couples, via a JAVA interface, an ordinary differential equation-based mass action kinetics model to compute intracellular Wnt/beta-catenin signaling with an agent-based model of mesendoderm migration across a fibronectin extracellular matrix substrate. The emergent cell behaviors in the simulation suggest the following properties of the system: maintaining the integrity of cell-to-cell contact signals is necessary for preventing fractionation of cells as they move, contact with the Fn substrate and the existence of a Fn gradient provides an extracellular feedback loop that governs migration speed, the incorporation of polarity signals is required for cells to migrate in the same direction, and a delicate balance of integrin and cadherin interactions is needed to reproduce experimentally observed migratory behaviors. CONCLUSION: Our computational framework couples two different spatial scales in biology: intracellular with multicellular. In our simulation, events at one scale have quantitative and dynamic impact on events at the other scale. This integration enables the testing and identification of key systems-level hypotheses regarding how signaling proteins affect overall tissue-level behavior during morphogenesis in an experimentally verifiable system. Applications of this approach extend to the study of tissue patterning processes that occur during adulthood and disease, such as tumorgenesis and atherogenesis.