Real-Time Spectral Library Matching for Sample Multiplexed Quantitative Proteomics.

Sample multiplexed quantitative proteomics assays have proved to be a highly versatile means to assay molecular phenotypes. Yet, stochastic precursor selection and precursor coisolation can dramatically reduce the efficiency of data acquisition and quantitative accuracy. To address this, intelligent data acquisition (IDA) strategies have recently been developed to improve instrument efficiency and quantitative accuracy for both discovery and targeted methods. Toward this end, we sought to develop and implement a new real-time spectral library searching (RTLS) workflow that could enable intelligent scan triggering and peak selection within milliseconds of scan acquisition. To ensure ease of use and general applicability, we built an application to read in diverse spectral libraries and file types from both empirical and predicted spectral libraries. We demonstrate that RTLS methods enable improved quantitation of multiplexed samples, particularly with consideration for quantitation from chimeric fragment spectra. We used RTLS to profile proteome responses to small molecule perturbations and were able to quantify up to 15% more significantly regulated proteins in half the gradient time compared to traditional methods. Taken together, the development of RTLS expands the IDA toolbox to improve instrument efficiency and quantitative accuracy for sample multiplexed analyses.

Interstudy repeatability of self-gated quantitative myocardial perfusion MRI.

PURPOSE: To evaluate the interstudy repeatability of multislice quantitative cardiovascular magnetic resonance myocardial blood flow (MBF), myocardial perfusion reserve (MPR), and extracellular volume (ECV). A unique saturation recovery self-gated acquisition was used for the perfusion scans. MATERIALS AND METHODS: An ungated golden angle radial turboFLASH pulse sequence was used to scan 10 subjects on two separate days on a 3T scanner. A single saturation pulse was followed by a set of four slices. Rest and hyperemia scans were acquired during free breathing. The images were reconstructed using an iterative algorithm with spatiotemporal constraints. The ungated images were retrospectively binned (self-gated) into near-systole and near-diastole. Deformable registration was performed to adjust for respiratory and residual cardiac motion, and the data were fit with a Fermi model to estimate the interstudy repeatability of quantitative self-gated MBF and MPR. RESULTS: The coefficient of variation (CoV) of the territorial MPR using the self-gated near-systole data was 18.6%. The self-gated near-diastole data gave less good CoV of MPR, equal to 46.2%. For MBFs, and using smaller (segmental) regions, the CoVs were 20.1% and 22.7% for the estimation of myocardial blood flow at stress and rest, respectively, using the self-gated near-systole data. The self-gated near-diastole data gave CoV = 48.6% and 44.9% for stress and rest. CONCLUSION: The self-gated free-breathing technique for quantification of myocardial blood flow showed good repeatability for near-systole, with results comparable to published studies on interstudy repeatability of quantitative myocardial perfusion MRI using ECG-gating and breath-holds. Self-gated near-diastole data results were less repeatable. J. Magn. Reson. Imaging 2016;43:1369-1378.

Quantification of myocardial perfusion with self-gated cardiovascular magnetic resonance.

BACKGROUND: Current myocardial perfusion measurements make use of an ECG-gated pulse sequence to track the uptake and washout of a gadolinium-based contrast agent. The use of a gated acquisition is a problem in situations with a poor ECG signal. Recently, an ungated perfusion acquisition was proposed but it is not known how accurately quantitative perfusion estimates can be made from such datasets that are acquired without any triggering signal. METHODS: An undersampled saturation recovery radial turboFLASH pulse sequence was used in 7 subjects to acquire dynamic contrast-enhanced images during free-breathing. A single saturation pulse was followed by acquisition of 4-5 slices after a delay of ~40 msec. This was repeated without pause and without any type of gating. The same pulse sequence, with ECG-gating, was used to acquire gated data as a ground truth. An iterative spatio-temporal constrained reconstruction was used to reconstruct the undersampled images. After reconstruction, the ungated images were retrospectively binned ("self-gated") into two cardiac phases using a region of interest based technique and deformably registered into near-systole and near-diastole. The gated and the self-gated datasets were then quantified with standard methods. RESULTS: Regional myocardial blood flow estimates (MBFs) obtained using self-gated systole (0.64 ± 0.26 ml/min/g), self-gated diastole (0.64 ± 0.26 ml/min/g), and ECG-gated scans (0.65 ± 0.28 ml/min/g) were similar. Based on the criteria for interchangeable methods listed in the statistical analysis section, the MBF values estimated from self-gated and gated methods were not significantly different. CONCLUSION: The self-gated technique for quantification of regional myocardial perfusion matched ECG-gated perfusion measurements well in normal subjects at rest. Self-gated systolic perfusion values matched ECG-gated perfusion values better than did diastolic values.

Highly accelerated cardiac cine phase-contrast MRI using an undersampled radial acquisition and temporally constrained reconstruction.

PURPOSE: To evaluate a method to enable single-slice or multiple-slice cine phase contrast (cine-PC) acquisition during a single breath-hold using a highly sparsified radial acquisition ordering and temporally constrained image reconstruction with a spatially varying temporal constraint. MATERIALS AND METHODS: Simulated and in vivo cine-PC datasets of the proximal ascending aorta were obtained at different acceleration factors using a view projection acquisition order optimized for temporally constrained reconstruction (TCR). Reconstruction of the sparse cine-PC data performed with TCR was compared to reconstructions using zero-filled regridding and temporal interpolation. RESULTS: TCR resulted in more accurate velocity measurements than regridding or temporal interpolation. In one dataset, TCR of undersampled in vivo data (16 views per cardiac phase) resulted in a peak systolic velocity within 3.3% of the value measured by Doppler ultrasound while shortening the scan time to 13 seconds. High temporal-resolution undersampled TCR was also compared lower temporal-resolution, more highly sampled, regridding in three normal volunteers. CONCLUSION: TCR proved to be an effective method for reconstructing undersampled radial PC data. Although TCR utilizes a temporal constraint, temporal blurring was minimized by using appropriate constraint weights in addition to a spatially varying temporal constraint. TCR allowed for the acquisition time to be reduced to the duration of a breath-hold, while still resulting in accurate velocity measurements.

The degree of left atrial structural remodeling impacts left ventricular ejection fraction in patients with atrial fibrillation.

OBJECTIVES: The extent of left atrial (LA) wall structural remodeling (fibrosis) detected by late gadolinium enhancement-magnetic resonance imaging (LGE-MRI) is correlated with advanced atrial fibrillation (AF). The concomitant occurrence of AF and left ventricular (LV) dysfunction is not uncommon. We studied the effect of LA fibrosis, a confounder of both AF and LV dysfunction, on LV ejection fraction (EF). STUDY DESIGN: For the analysis, we identified and included 384 patients from our retrospective AF database who underwent LGE-MRI and transthoracic echocardiography prior to AF ablation. Based on the degree of LA fibrosis, patients were categorized into four stages as: Utah 1 (<5% LA fibrosis), Utah 2 (5-20% fibrosis), Utah 3 (20-35% fibrosis), and Utah 4 (>35% fibrosis). RESULTS: The average pre-ablation LVEF was 60.5%±8.5% (n=24) in Utah stage 1 patients, 55.7%±10.3% (n=240) in Utah stage 2 patients, 51.7±11.5% (n=90) in Utah stage 3 patients, and 48.9%±11.6% (n=30) in Utah stage 4 patients (p<0.001, one-way ANOVA). The percentage of LA fibrosis was significantly negatively correlated to LVEF pre-ablation in a univariate analysis (p<0.001). In a multivariate model accounting for age, gender, AF type, and comorbidities such as diabetes and hypertension, Utah stage remained a significant predictor of pre-ablation EF (p<0.001). CONCLUSION: Patients with extensive LA fibrosis appear to have depressed LV function pre-ablation, suggesting that structural remodeling in the LA may also be triggering and promoting remodeling within the ventricular myocardium.

Higher degree of left atrial structural remodeling in patients with atrial fibrillation and left ventricular systolic dysfunction.

BACKGROUND: Catheter ablation significantly improves the left ventricular (LV) function in patients with atrial fibrillation (AF) and LV systolic dysfunction. In this study, we compared the degree of left atrial structural remodeling (LA-SRM) in patients with normal versus reduced LV ejection fraction (LVEF). We also studied the impact of LA-SRM on LVEF improvement in patients undergoing ablation of AF. METHOD AND RESULTS: We categorized 384 patients into 2 groups based on their cardiac function: reduced LVEF group (LVEF ≤50%; n = 105) and normal LVEF group (LVEF > 50%; n = 279). LVEF was determined prior and mean 8 ± 3 months after catheter ablation for AF. Percentage of LA-SRM was quantified using LGE-MRI and patients were classified into 4 groups based on the amount of structural remodeling in their LA wall: minimal ≤ 5%, mild = 5-20%, moderate = 20-35%, and extensive ≥ 35%. The average preablation LA-SRM (21.5 ± 13.2% vs 15.4 ± 10.0%; P < 0.001) was significantly higher in reduced LVEF group than normal LVEF group. Among the 105 patients with reduced LVEF, while there was a modest 11.7 ± 8.4% average increase in LVEF following ablation, the greatest increase was seen in patients with less extensive LA-SRM (minimal = 19.3 ± 5.1%, n = 3, P = 0.02 and mild = 16.6 ± 9.9%, n = 48, P < 0.001). Patients with moderate and extensive fibrosis had an average EF improvement of 8.7 ± 11.1% and 2.8 ± 6.4%, respectively (n = 39, P < 0.001 and n = 15, P = 0.11, respectively). CONCLUSION: Patients with LV systolic dysfunction displayed a comparatively greater LA-SRM than patients with normal LVEF. Patients with lesser LA-SRM experienced a greater improvement in LVEF after catheter ablation for AF.

Rapid ungated myocardial perfusion cardiovascular magnetic resonance: preliminary diagnostic accuracy.

BACKGROUND: Myocardial perfusion cardiovascular magnetic resonance (CMR) is a well-established method for detection of ischemic heart disease. However, ECG gating problems can result in image degradation and non-diagnostic scans, particularly in patients with arrhythmias. METHODS: A turboFLASH saturation recovery pulse sequence was used without any ECG triggering. One saturation pulse followed by 4-5 slices of undersampled radial k-space images was acquired rapidly, on the order of 40-50 msec per image. The acquisition of the set of 4-5 slices was continuously repeated approximately 4 times per second. An iterative constrained reconstruction method was used to reconstruct the ungated images. The ungated perfusion images were post-processed into three different sets of images (ungated, self-gated to near systole, and self-gated to near diastole). To test the ungated approach and compare the different processing methods, 8 patients scheduled for coronary angiography underwent stress and rest perfusion imaging with the ungated acquisition. Six patients had a history of atrial fibrillation (AF). Three blinded readers assessed image quality and presence/absence of disease. RESULTS: All 8 subjects successfully completed the perfusion CMR protocol and 7/8 underwent coronary angiography. Three patients were in atrial fibrillation during CMR. Overall, the CMR images were of high quality as assessed by the three readers. There was little difference in image quality between patients in AF compared to those in sinus rhythm (3.6±0.7 vs. 3.3±0.5). Stress/rest perfusion imaging showed normal perfusion in 4 patients, fixed perfusion defects in 2 patients, and reversible perfusion defects in 2 patients, corresponding with angiographic results. Pooled results from the independent readers gave a sensitivity of 0.92 (CI 0.65-0.99) and specificity of 0.92 (CI 0.65-0.99) for the detection of coronary artery disease using ungated perfusion imaging. The same sensitivity, and a specificity of 1 (CI 0.76-1), was achieved when the images were self-gated after acquisition into near systole or near diastole. CONCLUSIONS: Ungated radial dynamic perfusion CMR can give high quality imaging in patients in sinus rhythm and during atrial fibrillation. In this small cohort, high diagnostic accuracy was possible with this rapid perfusion imaging sequence. An ungated approach simplifies the acquisition and could expand the role of perfusion CMR to include patients with arrhythmia and those with gating problems.

Relationship between left atrial tissue structural remodelling detected using late gadolinium enhancement MRI and left ventricular hypertrophy in patients with atrial fibrillation.

AIMS: Therapeutic effectiveness of ablation of atrial fibrillation (AF) is related to cardiovascular comorbidities. We studied the relationship between left ventricular hypertrophy (LVH) and left atrial tissue structural remodelling (LA-SRM), in patients presenting for AF ablation. METHODS AND RESULTS: We identified 404 AF patients who received a late gadolinium enhancement magnetic resonance imaging (LGE-MRI) prior to catheter ablation. Left ventricular hypertrophy was defined as LV mass index >116 g/m(2) in men and >104 g/m(2) in women. One hundred and twenty-two patients were classified as the LVH group and 282 as the non-LVH group. We stratified patients into four stages based on their degree of LA-SRM (minimal, <5% fibrosis; mild, >5-20%; moderate, >20-35%; and extensive, >35%). All patients underwent catheter ablation with pulmonary vein isolation and posterior wall and septal debulking. The procedural outcome was monitored over a 1-year follow-up period. The mean LA-SRM was significantly higher in patients with LVH (19.4 ± 13.2%) than in non-LVH patients (15.3 ± 9.8%; P< 0.01). Patients with LVH generally had extensive LA-SRM (moderate and extensive stages; 38.5% of LVH group) as compared with non-LVH patients (23.1% of non-LVH group; P < 0.01). A Cox regression analysis showed that patients with LVH also had significantly higher AF recurrence rates than non-LVH patients (43.2 vs. 28%; P = 0.008) during the 1-year follow-up period post-ablation. CONCLUSION: Patients with LVH tend to have a significantly greater degree of LA-SRM, when compared with patients without LVH. Moreover, LA-SRM is a predictor for procedural success in patients undergoing AF ablation procedure.

Myocardial perfusion acquisition without magnetization preparation or gating.

Current myocardial perfusion MRI acquisitions are performed with a saturation recovery sequence, in large part to minimize sensitivity to arrhythmia. A new approach is proposed here where the images are acquired ungated at steady state without use of a saturation pulse. The data are acquired continuously and reach steady state after the first few images. A confluence of advances has made this new paradigm of an ungated steady-state acquisition possible-very rapid undersampled readouts with new reconstruction technologies permit enough measurements that continuous acquisition becomes a feasible approach. Gating can be applied retrospectively from a logged electrocardiogram (ECG) or with self-gating methods. In this work, simulations and measurements in a concentration phantom are used to demonstrate that similar contrast and signal can be obtained with the standard saturation recovery and the proposed spoiled gradient echo (SPGR) acquisition. Specifically, for a flip angle of 14° and a saturation recovery time of 80 ms, similar signals are acquired over a range of T(1) s that reflect realistic myocardial tissue concentrations. Preliminary results in one subject are presented to show the potential of this new approach. The method may allow for cine cardiac perfusion and more signal-to-noise ratio-efficient acquisitions.

Myocardial perfusion MRI with an undersampled 3D stack-of-stars sequence.

PURPOSE: To determine the feasibility of three-dimensional (3D) hybrid radial (stack-of-stars) MRI with spatiotemporal total variation (TV) constrained reconstruction for dynamic contrast enhanced myocardial perfusion imaging. METHODS: An ECG-triggered saturation recovery turboFLASH sequence with undersampled stack-of-stars sampling with spatiotemporal TV constrained reconstruction was developed for dynamic contrast enhanced myocardial perfusion imaging. Simulations were performed to study the dependence of the approach to steady state on flip angle and saturation recovery time for this stack-of-stars acquisition. Phantom studies were used to show the effect of the flip angle selection and imperfect spoiling on image qualities. Studies were done in three humans to test the feasibility of the approach for myocardial perfusion imaging. RESULTS: The simulation and phantom studies showed that imperfect spoiling and magnetization changes during the readout were a function of flip angle and nonoptimized selection of flip angle could degrade the images. Low flip angle acquisitions in the human subjects result in images with good quality similar to multislice radial 2D images. CONCLUSIONS: 3D stack-of-stars sampling with spatiotemporal TV constrained reconstruction provides a promising alternative for myocardial perfusion imaging.

Atrial fibrosis helps select the appropriate patient and strategy in catheter ablation of atrial fibrillation: a DE-MRI guided approach.

UNLABELLED: MRI for AF Patient Selection and Ablation Approach. INTRODUCTION: Left atrial (LA) fibrosis and ablation related scarring are major predictors of success in rhythm control of atrial fibrillation (AF). We used delayed enhancement MRI (DE-MRI) to stratify AF patients based on pre-ablation fibrosis and also to evaluate ablation-induced scarring in order to identify predictors of a successful ablation. METHODS AND RESULTS: One hundred and forty-four patients were staged by percent of fibrosis quantified with DE-MRI, relative to the LA wall volume: minimal or Utah stage 1; <5%, mild or Utah stage 2; 5-20%, moderate or Utah stage 3; 20-35%, and extensive or Utah stage 4; >35%. All patients underwent pulmonary vein (PV) isolation and posterior wall and septal debulking. Overall, LA scarring was quantified and PV antra were evaluated for circumferential scarring 3 months post ablation. LA scarring post ablation was comparable across the 4 stages. Most patients had either no (36.8%) or 1 PV (32.6%) antrum circumferentially scarred. Forty-two patients (29%) had recurrent AF over 283 ± 167 days. No recurrences were noted in Utah stage 1. Recurrence was 28% in Utah stage 2, 35% in Utah stage 3, and 56% in Utah stage 4. Recurrence was predicted by circumferential PV scarring in Utah stage 2 and by overall LA wall scarring in Utah stage 3. No recurrence predictors were identified in Utah stage 4. CONCLUSIONS: Circumferential PV antral scarring predicts ablation success in mild LA fibrosis, while posterior wall and septal scarring is needed for moderate fibrosis. This may help select the proper candidate and strategy in catheter ablation of AF.

A Practical Algorithm for Improving Localization and Quantification of Left Ventricular Scar.

Current approaches to classification of left ventricular scar rely on manual segmentation of myocardial borders and manual classification of scar tissue. In this paper, we propose an novel, semi-automatic approach to segment the left ventricular wall and classify scar tissue using a combination of modern image processing techniques. We obtained high-resolution magnetic resonance angiograms (MRA) and late-gadolinium enhanced magnetic resonance imaging (LGE-MRI) in 14 patients who had ventricular scar from a prior myocardial infarction. We applied (1) a level set-based segmentation approach using a combination of the MRA and LGE-MRI to segment the myocardium and then (2) an automated signal intensity algorithm (Otsu thresholding) to identify ventricular scar tissue. We compared results from both steps to those of expert observers. The LVgeometry using the semi-automated segmentation method had a mean overlap of 94% with the manual segmentations. The scar volumes obtained with the Otsu method correlated with the expert observer scar volumes (Dice comparison coefficient of 0.85± 0.11). This proof of concept segmentation pipeline provides a more objective method for identifying scar in the left ventricle than manual approaches.

The effect of obesity on regadenoson-induced myocardial hyperemia: a quantitative magnetic resonance imaging study.

The A2(A) receptor agonist, regadenoson, is increasingly used as a vasodilator during nuclear myocardial perfusion imaging. Regadenoson is administered as a single, fixed dose. Given the frequency of obesity in patients with symptoms of heart disease, it is important to know whether the fixed dose of regadenoson produces maximal coronary hyperemia in subjects of widely varying body size. Thirty subjects (12 female, 18 male, mean BMI 30.3 ± 6.5, range 19.6-46.6) were imaged on a 3T magnetic resonance scanner. Imaging with a saturation recovery radial turboFLASH sequence was done first at rest, then during adenosine infusion (140 µg/kg/min) and 30 min later with regadenoson (0.4 mg/5 ml bolus). A 5 cc/s injection of Gd-BOPTA was used for each perfusion sequence, with doses of 0.02, 0.03 and 0.03 mmol/kg, respectively. Analysis of the upslope of myocardial time-intensity curves and quantitative processing to obtain myocardial perfusion reserve (MPR) values were performed for each vasodilator. The tissue upslopes for adenosine and regadenoson matched closely (y = 1.1x + 0.03, r = 0.9). Mean MPR was 2.3 ± 0.6 for adenosine and 2.4 ± 0.9 for regadenoson (p = 0.14). There was good agreement between MPR measured with adenosine and regadenoson (y = 1.1x - 0.06, r = 0.7). The MPR values measured with both agents tended to be lower as BMI increased. There were no complications during administration of either agent. Regadenoson produced fewer side effects. Fixed dose regadenoson and weight adjusted adenosine produce similar measures of MPR in patients with a wide range of body sizes. Regadenoson is a potentially useful vasodilator for stress MRI studies.

MRI of the left atrium: predicting clinical outcomes in patients with atrial fibrillation.

Atrial fibrillation is a significant public health burden, with clinically, epidemiologically and economically significant repercussions. In the last decade, catheter ablation has provided an improvement in morbidity and quality of life, significantly reducing long-term healthcare costs and avoiding recurrences compared with drug therapy. Despite recent progress in techniques, current catheter ablation success rates fall short of expectations. Late gadolinium-enhancement cardiovascular MRI is a well-established tool to image the myocardium and, most specifically, the left atrium. Unique imaging protocols allow for left atrial structural remodeling and fibrosis assessment, which has been demonstrated to correlate with clinical outcomes after catheter ablation, assessment of the individual's risks of thromboembolic events, and effective imaging of patients with left atrial appendage thrombus. Late gadolinium-enhancement MRI aids in the individualized treatment of atrial fibrillation, stratifying recurrence risk and guiding specific ablation strategies. Real-time MRI offers significant safety and effectiveness profiles that would optimize the invasive treatment of atrial fibrillation.

Acquisition and reconstruction of undersampled radial data for myocardial perfusion magnetic resonance imaging.

PURPOSE: To improve myocardial perfusion magnetic resonance imaging (MRI) by reconstructing undersampled radial data with a spatiotemporal constrained reconstruction method (STCR). MATERIALS AND METHODS: The STCR method jointly reconstructs all of the time-frames for each slice. In 7 subjects at rest, on a 3-T scanner, the method was compared with a conventional (GRAPPA) Cartesian approach. RESULTS: Increased slice coverage was obtained, as compared with Cartesian acquisitions. On average, 10 slices were obtained per heartbeat for radial acquisitions (8 of which are suitable for visual analysis with the remaining 2 slices, in theory, usable for quantitative purposes), whereas 4 slices were obtained for the conventional Cartesian acquisitions. The new method was robust to interframe motion, unlike using Cartesian undersampling and STCR. STCR produced images with an image quality rating (1 for best and 5 for worst) of 1.7 +/- 0.5; the Cartesian images were rated 2.6 +/- 0.4 (P = 0.0006). A mean improvement of 44 (+/-17) in signal-to-noise (SNR) ratio and 46 (+22) in contrast-to-noise ratio (CNR) was observed for STCR. CONCLUSION: The new radial data acquisition and reconstruction scheme for dynamic myocardial perfusion imaging is a promising approach for obtaining significantly higher coverage and improved SNR ratios. Further testing of this approach is warranted during vasodilation in patients with coronary artery disease.