Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations.

Tsg101 UEV domain proteins are potential targets for virus infection therapy, especially for HIV and Ebola viruses. Peptides are key in curbing virus transmission, and cyclic peptides have a greater survival time than their linear peptides. To date, the accurate prediction of cyclic peptide-protein receptors binding conformations still is challenging because of high peptide flexibility. Here, a useful approach combined the global peptide docking, Gaussian accelerated molecular dynamics (GaMD), two-dimensional (2D) potential of mean force (PMF), normal molecular dynamics (cMD), and solvated interaction energy (SIE) techniques. Then we used this approach to investigate the binding conformations of UEV domain proteins with three cyclic peptides inhibitors. We reported the possible cyclic peptide-UEV domain protein binding conformations via 2D PMF free energy profiles and SIE free energy calculations. The residues Trp145, Tyr147, and Trp148 of the native cyclic peptide (CP1) indeed play essential roles in the cyclic peptides-UEV domain proteins interactions. Our findings might increase the accuracy of cyclic peptide-protein conformational prediction, which may facilitate cyclic peptide inhibitor design. Our approach is expected to further aid in addressing the challenges in cyclic peptide inhibitor design.

Analysis of accelerated 4D flow MRI in the murine aorta by radial acquisition and compressed sensing reconstruction.

Preclinical 4D flow MRI remains challenging and is restricted for parallel imaging acceleration due to the limited number of available receive channels. A radial acquisition with combined parallel imaging and temporal compressed sensing reconstruction was implemented to achieve accelerated preclinical 4D flow MRI. In order to increase the accuracy of the measured velocities, a quantitative evaluation of different temporal regularization weights for the compressed sensing reconstruction based on velocity instead of magnitude data is performed. A 3D radial retrospectively triggered phase contrast sequence with a combined parallel imaging and compressed sensing reconstruction with temporal regularization was developed. It was validated in a phantom and in vivo (C57BL/6 J mice), against an established fully sampled Cartesian sequence. Different undersampling factors (USFs [12, 15, 20, 30, 60]) were evaluated, and the effect of undersampling was analyzed in detail for magnitude and velocity data. Temporal regularization weights λ were evaluated for different USFs. Acceleration factors of up to 20 compared with full Nyquist sampling were achieved. The peak flow differences compared with the Cartesian measurement were the following: USF 12, 3.38%; USF 15, 4.68%; USF 20, 0.95%. The combination of 3D radial center-out trajectories and compressed sensing reconstruction is robust against motion and flow artifacts and can significantly reduce measurement time to 30 min at a resolution of 180 µm3 . Concisely, radial acquisition with combined compressed sensing and parallel imaging proved to be an excellent method for analyzing complex flow patterns in mice.

On the application of balanced steady-state free precession to MR microscopy.

OBJECTIVE: The applicability of the balanced steady-state free precession (bSSFP) sequence to the field of MR microscopy was investigated, since the potentially high SNR makes bSSFP attractive. However, particularly at ultra-high magnetic fields, a number of constraints emerge: the frequency sensitivity of the bSSFP signal, the duty cycle of the imaging gradients, and the intrinsic diffusion attenuation of the steady state due to the imaging gradients. MATERIALS AND METHODS: Optimization of the bSSFP sequence was performed on three imaging systems (7 T and 9.4 T) suited for MR microscopy. Since biological samples are often imaged in the very proximity of materials from sample containers/holder or devices such as electrodes, several microscopy phantoms representing such circumstances were fabricated and examined with 3D bSSFP. RESULTS: Artifact-free microscopic bSSFP images could be obtained with voxel sizes down to 16 µm × 16 µm × 78 µm and with an SNR gain of 25% over standard gradient echo images. CONCLUSION: With appropriate choice of phantom materials, optimization of the flip angle to the diffusion-attenuated steady state and protocols considering duty-cycle limitations, bSSFP can be a valuable tool in MR microscopy.

Preclinical 4D-flow magnetic resonance phase contrast imaging of the murine aortic arch.

PURPOSE: Cardiovascular diseases remain the number one death cause worldwide. Preclinical 4D flow phase contrast magnetic resonance imaging can provide substantial insights in the analysis of aortic pathophysiologies in various animal models. These insights may allow a better understanding of pathophysiologies, therapy monitoring, and can possibly be translated to humans. This study provides a framework to acquire the velocity field within the aortic arch. It analyses important flow values at different locations within the aortic arch. Imaging parameters with high temporal and spatial resolution are provided, that still allow combining this time-consuming method with other necessary imaging-protocols. METHODS: A new setup was established where a prospectively gated 4D phase contrast sequence is combined with a highly sensitive cryogenic coil on a preclinical magnetic resonance scanner. The sequence was redesigned to maintain a close to steady state condition of the longitudinal magnetization and hence to overcome steady state artifacts. Imaging parameters were optimized to provide high spatial and temporal resolution. Pathline visualizations were generated from the acquired velocity data in order to display complex flow patterns. RESULTS: Our setup allows data acquisition with at least two times the rate than that of previous publications based on Cartesian encoding, at an improved image quality. The "steady state" sequence reduces observed artifacts and provides uniform image intensity over the heart cycle. This made possible quantification of blood speed and wall shear stress (WSS) within the aorta and its branches. The highest velocities were observed in the ascending aorta with 137.5 ± 8 cm/s. Peak velocity values in the Brachiocephalic trunk were 57 ± 12 cm/s. Quantification showed that the peak flow occurs around 20 ms post R-wave in the ascending aorta. The highest mean axial wall shear stress was observed in the analysis plane between the left common carotid artery (LCCA) and the left subclavian artery. A stable image quality allows visualizing complex flow patterns by means of streamlines and for the first time, to the best of our knowledge, pathline visualizations from 4D flow MRI in mice. CONCLUSION: The described setup allows analyzing pathophysiologies in mouse models of cardiovascular diseases in the aorta and its branches with better image quality and higher spatial and temporal resolution than previous Cartesian publications. Pathlines provide an advanced analysis of complex flow patterns in the murine aorta. An imaging protocol is provided that offers the possibility to acquire the aortic arch at sufficiently high resolution in less than one hour. This allows the combination of the flow assessment with other multifunctional imaging protocols.

Pixel-wise derivation of pulmonary regurgitation index could influence clinical decision: A phase-contrast MR imaging study on patients with repaired tetralogy of Fallot.

PURPOSE: Regurgitant fraction (RF) measured from 2D phase-contrast MRI has been used as a standard to quantitate the degree of pulmonary regurgitation and serves as a determinant indicator of prognosis for tetralogy of Fallot after surgical repair. This study demonstrated the potential underestimate of RF using the conventional definition and its impact on clinical decision when backward flow occurred during systolic periods. METHODS: Quantitative flow parameters, including forward flow volume (FFV), backward flow volume (BFV), and RF were estimated by two approaches: One derived from conventional ROI-averaged curve (bulk quantity) and the other in a pixel-wise manner to spatially reflect inhomogeneous flow profile (pixel-wise quantity). Eccentricity at systolic peak (Eccsys) was adopted as an index reflecting spatial flow inhomogeneity. RESULTS: Flow parameters derived from ROI-averaged curves on main pulmonary artery were significantly smaller than that of pixel-wise measurement (P<0.001). Difference between RFbulk and RFpx for the group of Eccsys > 0.3 appears greater compared to the group with Eccsys < 0.3. Thirteen out of 68 RF values (19%) were underrated while using bulk analysis. CONCLUSIONS: The spatial-related flow parameters showed more consistency with the qualitative flow profile pattern for pulmonary arteries, and could be a decisive complement for diagnostic classification.

Effects of RF pulse profile and intra-voxel phase dispersion on MR fingerprinting with balanced SSFP readout.

PURPOSE: To investigate possible errors in T1 and T2 quantification via MR fingerprinting with balanced steady-state free precession readout in the presence of intra-voxel phase dispersion and RF pulse profile imperfections, using computer simulations based on Bloch equations. MATERIALS AND METHODS: A pulse sequence with TR changing in a Perlin noise pattern and a nearly sinusoidal pattern of flip angle following an initial 180-degree inversion pulse was employed. Gaussian distributions of off-resonance frequency were assumed for intra-voxel phase dispersion effects. Slice profiles of sinc-shaped RF pulses were computed to investigate flip angle profile influences. Following identification of the best fit between the acquisition signals and those established in the dictionary based on known parameters, estimation errors were reported. In vivo experiments were performed at 3T to examine the results. RESULTS: Slight intra-voxel phase dispersion with standard deviations from 1 to 3Hz resulted in prominent T2 under-estimations, particularly at large T2 values. T1 and off-resonance frequencies were relatively unaffected. Slice profile imperfections led to under-estimations of T1, which became greater as regional off-resonance frequencies increased, but could be corrected by including slice profile effects in the dictionary. Results from brain imaging experiments in vivo agreed with the simulation results qualitatively. CONCLUSION: MR fingerprinting using balanced SSFP readout in the presence of intra-voxel phase dispersion and imperfect slice profile leads to inaccuracies in quantitative estimations of the relaxation times.

Effects of B Value on Quantification of Rapid Diffusion Kurtosis Imaging in Normal and Acute Ischemic Brain Tissues.

PURPOSE: Diffusion kurtosis imaging (DKI) has been widely used to characterize brain tissue alterations. Diffusion-weighting factor or b value plays an important role in the measurement of rapid DKI and may have influential effects on them. The purpose of this study was to investigate the effects of b value on rapid DKI indices in normal and acute ischemic brain tissues. MATERIALS AND METHODS: This study enrolled 10 healthy subjects and 4 acute ischemic stroke patients. Three repeated DKI data with 6 high b values (500, 750, 1000, 1500, 2000, 3000 s/mm) were acquired from healthy subjects, whereas nonrepeated DKI data with 3 high b values (1000, 2000, 3000 s/mm) were acquired from ischemic stroke patients. The DKI datasets were decomposed into several rapid DKI datasets consisting of 1 b0 and 2 high b values for comparisons. RESULTS: The results showed that b value significantly impacted the reproducibility and accuracy of DKI indices. The comparisons demonstrated that DKI with b = (0, 1000, 3000) s/mm exhibited more reproducible and accurate DKI indices than other DKI datasets in normal brain tissues, and similar results were noticed in acute ischemic brain tissue. CONCLUSIONS: We concluded that b value significantly impacted the quantification of DKI indices in both normal and acute ischemic brain tissues.

Simultaneous detection of valine and lactate using MEGA-PRESS editing in pyogenic brain abscess.

Valine and lactate have been recognized as important metabolic markers to diagnose brain abscess by means of MRS. However, in vivo unambiguous detection and quantification is hampered by macromolecular contamination. In this work, MEGA-PRESS difference editing of valine and lactate is proposed. The method is validated in vitro and applied for quantitative in vivo experiments in one healthy subject and two brain abscess patients. It is demonstrated that with this technique the overlapping lipid signal can be reduced by more than an order of magnitude and thus the robustness of valine and lactate detection in vivo can be enhanced. Quantification of the two abscess MEGA-PRESS spectra yielded valine/lactate concentration ratios of 0.10 and 0.27. These ratios agreed with the concentration ratios determined from concomitantly acquired short-TE PRESS data and were in line with literature values. The quantification accuracy of lactate (as measured with Cramér-Rao lower bounds in LCModel processing) was better for MEGA-PRESS than for short-TE PRESS in all acquired in vivo datasets. The Cramér-Rao lower bounds of valine were only better for MEGA-PRESS in one of the two abscess cases, while in the other case coediting of isoleucine confounded the quantification in the MEGA-PRESS analysis. MEGA-PRESS and short-TE PRESS should be combined for unambiguous quantification of amino acids in abscess measurements. Simultaneous valine/lactate MEGA-PRESS editing might benefit the distinction of brain abscesses from tumors, and further categorization of bacteria with reasonable sensitivity and specificity.

Proton MR spectroscopy in patients with pyogenic brain abscess: MR spectroscopic imaging versus single-voxel spectroscopy.

PURPOSE: Single-voxel spectroscopy (SVS) has been the gold standard technique to diagnose the pyogenic abssess. Two-dimensional magnetic resonance spectroscopic imaging (MRSI) is able to provide spatial distribution of metabolic concentration, and is potentially more suitable for differential diagnosis between abscess and necrotic tumors. Therefore, the purpose of this study was to evaluate the equivalence of MRSI and SVS in the detection of the metabolites in pyogenic brain abscesses. MATERIALS AND METHODS: Forty-two patients with pyogenic abscesses were studied by using both SVS and MRSI methods. Two neuroradiologists reviewed the MRS data independently. A κ value was calculated to express inter-reader agreement of the abscesses metabolites, and a correlation coefficient was calculated to show the similarity of two spectra. After consensus judgment of two readers, the binary value of metabolites of pyogenic abscesses (presence or absence) was compared between SVS and MRSI. RESULTS: The consistency of spectral interpretation of the two readers was very good (κ ranged from 0.95 to 1), and the similarity of two spectra was also very high (cc=0.9±0.05). After consensus judgment of two readers, the sensitivities of MRSI ranged from 91% (acetate) to 100% (amino acids, succinate, lactate, lipid), and the specificities of MRSI were 100% for detecting all metabolites with SVS as reference. CONCLUSION: SVS and MRSI provide similar metabolites in the cavity of pyogenic brain abscess. With additional metabolic information of cavity wall and contralateral normal-appearing brain tissue, MRSI would be a more suitable technique to differentiate abscesses from necrotic tumors.

Reduced hippocampal glutamate-glutamine levels in irritable bowel syndrome: preliminary findings using magnetic resonance spectroscopy.

OBJECTIVES: Enhanced stress responsiveness is an important pathophysiological factor in irritable bowel syndrome (IBS), suggesting the presence of a dysregulated hypothalamic-pituitary-adrenal (HPA) axis. A possible mechanism involves maladaption of the feedback mechanism of the HPA axis. We hypothesized that hippocampus, a key brain region providing inhibitory feedback to the HPA axis, would exhibit reduced excitatory glutamatergic neurotransmission and reduced N-acetyl-aspartate (NAA; a marker of neuronal integrity) levels in IBS patients. METHODS: In this preliminary study, proton magnetic resonance spectroscopy was used to quantify absolute concentrations of metabolites in bilateral hippocampi of 15 IBS patients without significant psychiatric comorbidity and 15 age-matched controls. RESULTS: The main finding was a reduction in hippocampal glutamate-glutamine (Glx) in IBS patients. Furthermore, Glx concentrations were inversely related to emotional stress indicators in patients only. No difference was found between subject groups for other metabolite concentrations, including NAA. However, an elevated myo-inositol (mI)/NAA ratio was found in IBS patients. CONCLUSIONS: Our results provide preliminary evidence for the presence of abnormal hypofunction of hippocampal glutamatergic neurotransmission in IBS patients without psychiatric comorbidity, possibly as a result of the chronic pain. This supports the notion of an imbalance in regulatory brain regions in this subgroup of IBS patients. The inverse relationship between Glx and emotional stress indicators is in agreement with the inhibitory role of hippocampus on the stress system and suggests a sensitization of the mechanism to emotional arousal. The elevated mI/NAA ratio in IBS patients further suggests the presence of hippocampal glial proliferation and remodeling.

Short-TE proton magnetic resonance spectroscopy investigation in adolescents with attention-deficit hyperactivity disorder.

In this study, short echo time (1)H-magnetic resonance spectroscopy (MRS) was applied for quantification of neurometabolites using the LC Model algorithm in Taiwanese adolescents with attention-deficit hyperactivity disorder (ADHD). Proton magnetic resonance spectra were acquired bilaterally on the prefrontal area (part of the anterior cingulate gyrus and part of the medial frontal gyrus) in 15 adolescents with ADHD (average age of 13.88years) and 22 controls (average age of 14.85years). Absolute metabolite levels and ratios relative to creatine plus phosphocreatine (Cr+PCr) were obtained to be compared between groups. Results showed that adolescents with ADHD had significantly lower mean right prefrontal levels of Cr+PCr as compared with the controls. No significant differences between groups were noted in the remainder of the prefrontal metabolites. As for the group comparison of relative ratios, the N-acetylaspartate/Cr+PCr ratio was significantly higher in the right prefrontal regions of ADHD adolescents. This finding provides evidence of a right prefrontal neurochemical alteration in ADHD adolescents, which is consistent with current ADHD theory of prefrontal neuropathology with developmental mechanism. In addition, it highlights the importance of the method in interpretation of MRS findings in the context of ADHD.

Proton magnetic resonance spectroscopy and diffusion-weighted imaging in intracranial cystic mass lesions.

BACKGROUND: The differential diagnosis of various intracranial cystic lesions is sometimes difficult on the basis of CT or MRI findings. Our objective was to evaluate (1)H MRS and DWI in the differential diagnosis of these lesions and in comparison with conventional MRI. METHODS: Fifty patients with intracranial cystic lesions (21 pyogenic abscesses, 23 tumor cysts, 3 epidermoid cysts, and 3 arachnoid cysts) were evaluated with conventional MRI, DWI, and in vivo (1)H MRS. Preoperative diagnosis of the lesions was based on the results of DWI and in vivo MRS. All DWI and (1)H MRS studies were performed with a clinical 1.5-T system. The DWI was performed using single-shot spin-echo echo-planar pulse sequence with b = 1000 s/mm(2). The ADC value was measured. Diagnostic accuracy of conventional MRI, DWI, and in vivo (1)H MRS was calculated with respect to a final diagnosis of brain abscess vs nonabscess cystic tumor. RESULTS: Lactate and cytosolic amino acids with/without succinate, acetate, and alanine were observed in 18 of 21 cases of abscesses on MRS. In 3 cases of epidermoid cysts, lactate was observed and could be differentiated from 3 cases of arachnoid cysts, which showed only minimal lactate. Only lactate was seen in 14 of 23 patients with tumor cysts, whereas both lipid/lactate and choline were visible in 9 patients with tumor cysts. Increased signal was seen in 20 of 21 patients with abscesses and 3 patients with epidermoid cysts on DWI. Decreased signal was observed in 22 of 23 patients with tumor cysts and 3 patients with arachnoid cyst on DWI. Diagnostic accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of conventional MRI for the differentiation of brain abscess from nonabscess cystic tumor were 61.4%, 61.9%, 60.9%, 59.1%, and 63.6%, respectively, whereas they were 93.2%, 85.7%, 100%, 100%, and 88.5% with MRS; 95.5%, 95.2%, 95.7%, 95.2%, and 95.7% with DWI; and 97.7%, 95.2%, 100%, 100%, and 95.8% with MRS and DWI. Magnetic resonance imaging, when combined with in vivo MRS and DWI, accurately predicted the diagnosis in 47 (94%) of 50 and 48 (96%) of 50 of the cases, respectively. CONCLUSIONS: Proton MRS and DWI are useful as additional diagnostic modalities in differentiating intracranial cystic lesions. Combination of DWI with calculated ADC values and metabolite spectrum acquired by MRS add more information to MRI in the differentiation of intracranial cystic mass lesions.

Fast mapping of the T2 relaxation time of cerebral metabolites using proton echo-planar spectroscopic imaging (PEPSI).

Metabolite T2 is necessary for accurate quantification of the absolute concentration of metabolites using long-echo-time (TE) acquisition schemes. However, lengthy data acquisition times pose a major challenge to mapping metabolite T2. In this study we used proton echo-planar spectroscopic imaging (PEPSI) at 3T to obtain fast T2 maps of three major cerebral metabolites: N-acetyl-aspartate (NAA), creatine (Cre), and choline (Cho). We showed that PEPSI spectra matched T2 values obtained using single-voxel spectroscopy (SVS). Data acquisition for 2D metabolite maps with a voxel volume of 0.95 ml (32 x 32 image matrix) can be completed in 25 min using five TEs and eight averages. A sufficient spectral signal-to-noise ratio (SNR) for T2 estimation was validated by high Pearson's correlation coefficients between logarithmic MR signals and TEs (R2 = 0.98, 0.97, and 0.95 for NAA, Cre, and Cho, respectively). In agreement with previous studies, we found that the T2 values of NAA, but not Cre and Cho, were significantly different between gray matter (GM) and white matter (WM; P < 0.001). The difference between the T2 estimates of the PEPSI and SVS scans was less than 9%. Consistent spatial distributions of T2 were found in six healthy subjects, and disagreement among subjects was less than 10%. In summary, the PEPSI technique is a robust method to obtain fast mapping of metabolite T2.

Application of model-free analysis in the MR assessment of pulmonary perfusion dynamics.

Dynamic contrast-enhanced (DCE) MRI has been used to quantitatively evaluate pulmonary perfusion based on the assumption of a gamma-variate function and an arterial input function (AIF) for deconvolution. However, these assumptions may be too simplistic and may not be valid in pathological conditions, especially in patients with complex inflow patterns (such as in congenital heart disease). Exploratory data analysis methods make minimal assumptions on the data and could overcome these pitfalls. In this work, two temporal clustering methods--Kohonen clustering network (KCN) and Fuzzy C-Means (FCM)--were concatenated to identify pixel time-course patterns. The results from seven normal volunteers show that this technique is superior for discriminating vessels and compartments in the pulmonary circulation. Patient studies with five cases of acquired or congenital pulmonary perfusion disorders demonstrate that pathologies can be highlighted in a concise map that combines information of the mean transit time (MTT) and pulmonary blood volume (PBV). The method was found to provide greater insight into the perfusion dynamics that might be overlooked by current model-based analyses, and may serve as a basis for optimal hemodynamic quantitative modeling of the interrogated perfusion compartments.

MR ventriculocisternography by using 3D balanced steady-state free precession imaging: technical note.

This study investigated the effects of flip angle setting in 3D balanced steady-state free precession (SSFP) imaging on CSF-parenchyma contrast and section aliasing artifacts. Theoretical derivations indicated that the extent of section aliasing artifacts decreased as the flip angle was lowered, at the expense of a sacrifice in CSF-parenchyma contrast. Experimental data agreed closely with theoretical predictions. A flip angle of about 40 degrees is therefore recommended for 3D balanced SSFP MR ventriculocisternography.

Fat and water separation in balanced steady-state free precession using the Dixon method.

In this work the feasibility of separating fat and water signals using the balanced steady-state free precession (SSFP) technique is demonstrated. The technique is based on the observation (Scheffler and Hennig, Magnetic Resonance in Medicine 2003;49:395-397) that at the nominal values of TE = TR/2 in SSFP imaging, phase coherence can be achieved at essentially only two orientations (0 degrees and 180 degrees ) relative to the RF pulses in the rotating frame, under the assumption of TR << T2, and independently of the SSFP angle. This property allows in-phase and out-of-phase SSFP images to be obtained by proper choices of the center frequency offset, and thus allows the Dixon subtraction method to be utilized for effective fat-water separation. The TR and frequency offset for optimal fat-water separation are derived from theories. Experimental results from healthy subjects, using a 3.0 Tesla system, show that nearly complete fat suppression can be accomplished.