Glycyl Radical Enzymes and Sulfonate Metabolism in the Microbiome.

Sulfonates include diverse natural products and anthropogenic chemicals and are widespread in the environment. Many bacteria can degrade sulfonates and obtain sulfur, carbon, and energy for growth, playing important roles in the biogeochemical sulfur cycle. Cleavage of the inert sulfonate C-S bond involves a variety of enzymes, cofactors, and oxygen-dependent and oxygen-independent catalytic mechanisms. Sulfonate degradation by strictly anaerobic bacteria was recently found to involve C-S bond cleavage through O2-sensitive free radical chemistry, catalyzed by glycyl radical enzymes (GREs). The associated discoveries of new enzymes and metabolic pathways for sulfonate metabolism in diverse anaerobic bacteria have enriched our understanding of sulfonate chemistry in the anaerobic biosphere. An anaerobic environment of particular interest is the human gut microbiome, where sulfonate degradation by sulfate- and sulfite-reducing bacteria (SSRB) produces H2S, a process linked to certain chronic diseases and conditions.

Expression of accessory genes in Salmonella requires the presence of the Gre factors.

Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.

A predictor-corrector phase unwrapping algorithm for temporally undersampled gradient-echo MRI.

PURPOSE: To develop a method for unwrapping temporally undersampled and nonlinear gradient recalled echo (GRE) phase. THEORY AND METHODS: Temporal unwrapping is performed as a sequential one step prediction of the echo phase, followed by a correction to the nearest integer wrap-count. A spatio-temporal extension of the 1D predictor corrector unwrapping (PCU) algorithm improves the prediction accuracy, and thereby maintains spatial continuity. The proposed method is evaluated using numerical phantom, physical phantom, and in vivo brain data at both 3 T and 9.4 T. The unwrapping performance is compared with the state-of-the-art temporal and spatial unwrapping algorithms, and the spatio-temporal iterative virtual-echo based Nyquist sampled (iVENyS) algorithm. RESULTS: Simulation results showed significant reduction in unwrapping errors at higher echoes compared with the state-of-the-art algorithms. Similar to the iVENyS algorithm, the PCU algorithm was able to generate spatially smooth phase images for in vivo data acquired at 3 T and 9.4 T, bypassing the use of additional spatial unwrapping step. A key advantage over iVENyS algorithm is the superior performance of PCU algorithm at higher echoes. CONCLUSION: PCU algorithm serves as a robust phase unwrapping method for temporally undersampled and nonlinear GRE phase, particularly in the presence of high field gradients.

Whole-cerebrum guanidino and amide CEST mapping at 3 T by a 3D stack-of-spirals gradient echo acquisition.

PURPOSE: To develop a 3D, high-sensitivity CEST mapping technique based on the 3D stack-of-spirals (SOS) gradient echo readout, the proposed approach was compared with conventional acquisition techniques and evaluated for its efficacy in concurrently mapping of guanidino (Guan) and amide CEST in human brain at 3 T, leveraging the polynomial Lorentzian line-shape fitting (PLOF) method. METHODS: Saturation time and recovery delay were optimized to achieve maximum CEST time efficiency. The 3DSOS method was compared with segmented 3D EPI (3DEPI), turbo spin echo, and gradient- and spin-echo techniques. Image quality, temporal SNR (tSNR), and test-retest reliability were assessed. Maps of Guan and amide CEST derived from 3DSOS were demonstrated on a low-grade glioma patient. RESULTS: The optimized recovery delay/saturation time was determined to be 1.4/2 s for Guan and amide CEST. In addition to nearly doubling the slice number, the gradient echo techniques also outperformed spin echo sequences in tSNR: 3DEPI (193.8 ± 6.6), 3DSOS (173.9 ± 5.6), and GRASE (141.0 ± 2.7). 3DSOS, compared with 3DEPI, demonstrated comparable GuanCEST signal in gray matter (GM) (3DSOS: [2.14%-2.59%] vs. 3DEPI: [2.15%-2.61%]), and white matter (WM) (3DSOS: [1.49%-2.11%] vs. 3DEPI: [1.64%-2.09%]). 3DSOS also achieves significantly higher amideCEST in both GM (3DSOS: [2.29%-3.00%] vs. 3DEPI: [2.06%-2.92%]) and WM (3DSOS: [2.23%-2.66%] vs. 3DEPI: [1.95%-2.57%]). 3DSOS outperforms 3DEPI in terms of scan-rescan reliability (correlation coefficient: 3DSOS: 0.58-0.96 vs. 3DEPI: -0.02 to 0.75) and robustness to motion as well. CONCLUSION: The 3DSOS CEST technique shows promise for whole-cerebrum CEST imaging, offering uniform contrast and robustness against motion artifacts.

Improved test-retest reliability of R 2 * $$ {\mathrm{R}}_2

PURPOSE: This study aimed to evaluate the potential of 3D EPI for improving the reliability of T 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted data and quantification of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ decay rate and susceptibility (χ) compared with conventional gradient-echo (GRE)-based acquisition. METHODS: Eight healthy subjects in a wide age range were recruited. Each subject received repeated scans for both GRE and EPI acquisitions with an isotropic 1 mm resolution at 3 T. Maps of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ were quantified, and their interscan differences were used to evaluate the test-retest reliability. Interprotocol differences of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ between GRE and EPI were also measured voxel by voxel and in selected regions of interest to test the consistency between the two acquisition methods. RESULTS: The quantifications of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ using EPI protocols showed increased test-retest reliability with higher EPI factors up to 5 as performed in the experiment and were consistent with those based on GRE. CONCLUSION: The result suggests that multishot multi-echo 3D EPI can be a useful alternative acquisition method for T 2 * $$ {\mathrm{T}}_2^{\ast } $$ -weighted MRI and quantification of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ and χ with reduced scan time, improved test-retest reliability, and similar accuracy compared with commonly used 3D GRE.

Global regulator IrrE on stress tolerance: a review.

Stress tolerance is a vital attribute for all living beings to cope with environmental adversities. IrrE (also named PprI) from Deinococcus radiodurans enhances resistance to extreme radiation stress by functioning as a global regulator, mediating the transcription of genes involved in deoxyribonucleic acid (DNA) damage response (DDR). The expression of IrrE augmented the resilience of various species to heat, radiation, oxidation, osmotic stresses and inhibitors, encompassing bacterial, fungal, plant, and mammalian cells. Moreover, IrrE was employed in a global regulator engineering strategy to broaden its applications in stress tolerance. The regulatory impacts of heterologously expressed IrrE have been investigated at the molecular and systems level, including the regulation of genes, proteins, modules, or pathways involved in DNA repair, detoxification proteins, protective molecules, native regulators and other aspects. In this review, we discuss the regulatory role and mechanism of IrrE in the antiradiation response of D. radiodurans. Furthermore, the applications and regulatory effects of heterologous expression of IrrE to enhance abiotic stress tolerance are summarized in particular.

Comparing CT-Like Images Based on Ultra-Short Echo Time and Gradient Echo T1-Weighted MRI Sequences for the Assessment of Vertebral Disorders Using Histology and True CT as the Reference Standard.

BACKGROUND: Several magnetic resonance (MR) techniques have been suggested for radiation-free imaging of osseous structures. PURPOSE: To compare the diagnostic value of ultra-short echo time and gradient echo T1-weighted MRI for the assessment of vertebral pathologies using histology and computed tomography (CT) as the reference standard. STUDY TYPE: Prospective. SUBJECTS: Fifty-nine lumbar vertebral bodies harvested from 20 human cadavers (donor age 73 ± 13 years; 9 male). FIELD STRENGTH/SEQUENCE: Ultra-short echo time sequence optimized for both bone (UTEb) and cartilage (UTEc) imaging and 3D T1-weighted gradient-echo sequence (T1GRE) at 3 T; susceptibility-weighted imaging (SWI) gradient echo sequence at 1.5 T. CT was performed on a dual-layer dual-energy CT scanner using a routine clinical protocol. ASSESSMENT: Histopathology and conventional CT were acquired as standard of reference. Semi-quantitative and quantitative morphological features of degenerative changes of the spines were evaluated by four radiologists independently on CT and MR images independently and blinded to all other information. Features assessed were osteophytes, endplate sclerosis, visualization of cartilaginous endplate, facet joint degeneration, presence of Schmorl's nodes, and vertebral dimensions. Vertebral disorders were assessed by a pathologist on histology. STATISTICAL TESTS: Agreement between T1GRE, SWI, UTEc, and UTEb sequences and CT imaging and histology as standard of reference were assessed using Fleiss' κ and intra-class correlation coefficients, respectively. RESULTS: For the morphological assessment of osteophytes and endplate sclerosis, the overall agreement between SWI, T1GRE, UTEb, and UTEc with the reference standard (histology combined with CT) was moderate to almost perfect for all readers (osteophytes: SWI, κ range: 0.68-0.76; T1GRE: 0.92-1.00; UTEb: 0.92-1.00; UTEc: 0.77-0.85; sclerosis: SWI, κ range: 0.60-0.70; T1GRE: 0.77-0.82; UTEb: 0.81-0.92; UTEc: 0.61-0.71). For the visualization of the cartilaginous endplate, UTEc showed the overall best agreement with the reference standard (histology) for all readers (κ range: 0.85-0.93). DATA CONCLUSIONS: Morphological assessment of vertebral pathologies was feasible and accurate using the MR-based bone imaging sequences compared to CT and histopathology. T1GRE showed the overall best performance for osseous changes and UTEc for the visualization of the cartilaginous endplate. LEVEL OF EVIDENCE: 1 TECHNICAL EFFICACY: Stage 2.

Ferumoxytol-Enhanced Cardiac Cine MRI Reconstruction Using a Variable-Splitting Spatiotemporal Network.

BACKGROUND: Balanced steady-state free precession (bSSFP) imaging is commonly used in cardiac cine MRI but prone to image artifacts. Ferumoxytol-enhanced (FE) gradient echo (GRE) has been proposed as an alternative. Utilizing the abundance of bSSFP images to develop a computationally efficient network that is applicable to FE GRE cine would benefit future network development. PURPOSE: To develop a variable-splitting spatiotemporal network (VSNet) for image reconstruction, trained on bSSFP cine images and applicable to FE GRE cine images. STUDY TYPE: Retrospective and prospective. SUBJECTS: 41 patients (26 female, 53 ± 19 y/o) for network training, 31 patients (19 female, 49 ± 17 y/o) and 5 healthy subjects (5 female, 30 ± 7 y/o) for testing. FIELD STRENGTH/SEQUENCE: 1.5T and 3T, bSSFP and GRE. ASSESSMENT: VSNet was compared to VSNet with total variation loss, compressed sensing and low rank methods for 14× accelerated data. The GRAPPA×2/×3 images served as the reference. Peak signal-to-noise-ratio (PSNR), structural similarity index (SSIM), left ventricular (LV) and right ventricular (RV) end-diastolic volume (EDV), end-systolic volume (ESV), and ejection fraction (EF) were measured. Qualitative image ranking and scoring were independently performed by three readers. Latent scores were calculated based on scores of each method relative to the reference. STATISTICS: Linear mixed-effects regression, Tukey method, Fleiss' Kappa, Bland-Altman analysis, and Bayesian categorical cumulative probit model. A P-value <0.05 was considered statistically significant. RESULTS: VSNet achieved significantly higher PSNR (32.7 ± 0.2), SSIM (0.880 ± 0.004), rank (2.14 ± 0.06), and latent scores (-1.72 ± 0.22) compared to other methods (rank >2.90, latent score < -2.63). Fleiss' Kappa was 0.52 for scoring and 0.61 for ranking. VSNet showed no significantly different LV and RV ESV (P = 0.938) and EF (P = 0.143) measurements, but statistically significant different (2.62 mL) EDV measurements compared to the reference. CONCLUSION: VSNet produced the highest image quality and the most accurate functional measurements for FE GRE cine images among the tested 14× accelerated reconstruction methods. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY: Stage 1.

CT-like images based on T1-weighted gradient echo MRI sequences for the assessment of fractures of the hand and wrist compared to CT.

OBJECTIVE: To evaluate the performance of a 3D T1-weighted gradient-echo (3D T1GRE) computed tomography (CT)-like magnetic resonance imaging (MRI) sequence for detecting and assessing wrist and hand fractures compared to conventional CT. METHODS: Subjects with acute wrist or hand fracture in CT underwent additional 3 T MRI including a CT-like 3D T1GRE sequence and were compared to patients without fractures. Two radiologists assessed fracture morphology on both modalities according to the Arbeitsgemeinschaft Osteosynthese (AO) and graded image quality and diagnostic confidence on a 5-point Likert scale. Besides diagnostic test evaluation, differences in image quality and diagnostic confidence between CT-like MRI and CT were calculated using the Wilcoxon test. Agreement of AO classification between modalities and readers was assessed using Cohen's Kappa. RESULTS: Twenty-eight patients with 43 fractures and 43 controls were included. Image quality (3D T1GRE 1.19 ± 0.37 vs. CT 1.22 ± 0.42; p = 0.65) and diagnostic confidence (3D T1GRE 1.28 ± 0.53 vs. CT 1.28 ± 0.55; p = 1.00) were rated excellent for both modalities. Regarding the AO classification, intra- (rater 1 and rater 2, κ = 0.89; 95% CI 0.80-0.97) and interrater agreement were excellent (3D T1GRE, κ = 0.82; 95% CI, 0.70-0.93; CT, κ = 0.85; 95% CI, 0.75-0.94). CT-like MRI showed excellent sensitivity, specificity and accuracy for fracture detection (reader 1: 1.00, 0.92, 0.96; reader 2: 0.98, 0.94, 0.96). CONCLUSION: CT-like MRI is a comparable alternative to CT for assessing hand and wrist fractures, offering the advantage of avoiding radiation exposure.

Diffusion weighted hyperpolarized 129 Xe MRI of the lung with 2D and 3D (FLORET) spiral.

PURPOSE: To enable efficient hyperpolarized 129 Xe diffusion imaging using 2D and 3D (Fermat Looped, ORthogonally Encoded Trajectories, FLORET) spiral sequences and demonstrate that 129 Xe ADCs obtained using these sequences are comparable to those obtained using a conventional, 2D gradient-recalled echo (GRE) sequence. THEORY AND METHODS: Diffusion-weighted 129 Xe MRI (b-values = 0, 7.5, 15 s/cm2 ) was performed in four healthy volunteers and one subject with lymphangioleiomyomatosis using slice-selective 2D-GRE (scan time = 15 s), slice-selective 2D-Spiral (4 s), and 3D-FLORET (16 s) sequences. Experimental SNRs from b-value = 0 images ( SNR 0 EX $$ SNR{0}_{EX} $$ ) and mean ADC values were compared across sequences. In two healthy subjects, a second b = 0 image was acquired using the 2D-Spiral sequence to map flip angle and correct RF-induced, hyperpolarized signal decay at the voxel level, thus improving regional ADC estimates. RESULTS: Diffusion-weighted images from spiral sequences displayed image quality comparable to 2D-GRE and produced sufficient SNR 0 EX $$ SNR{0}_{EX} $$ (16.8 ± 3.8 for 2D-GRE, 21.2 ± 3.5 for 2D-Spiral, 20.4 ± 3.5 for FLORET) to accurately calculate ADC. Whole-lung means and SDs of ADC obtained via spiral were not significantly different (P > 0.54) from those obtained via 2D-GRE. Finally, 2D-Spiral images were corrected for signal decay, which resulted in a whole-lung mean ADC decrease of ˜15%, relative to uncorrected images. CONCLUSIONS: Relative to GRE, efficient spiral sequences allow 129 Xe diffusion images to be acquired with isotropic lung coverage (3D), higher SNR $$ SNR $$ (2D and 3D), and three-fold faster (2D) within a single breath-hold. In turn, shortened breath-holds enable flip-angle mapping, and thus, allow RF-induced signal decay to be corrected, increasing ADC accuracy.

Motion-resolved fat-fraction mapping with whole-heart free-running multiecho GRE and pilot tone.

PURPOSE: To develop a free-running 3D radial whole-heart multiecho gradient echo (ME-GRE) framework for cardiac- and respiratory-motion-resolved fat fraction (FF) quantification. METHODS: (NTE = 8) readouts optimized for water-fat separation and quantification were integrated within a continuous non-electrocardiogram-triggered free-breathing 3D radial GRE acquisition. Motion resolution was achieved with pilot tone (PT) navigation, and the extracted cardiac and respiratory signals were compared to those obtained with self-gating (SG). After extra-dimensional golden-angle radial sparse parallel-based image reconstruction, FF, R2 *, and B0 maps, as well as fat and water images were generated with a maximum-likelihood fitting algorithm. The framework was tested in a fat-water phantom and in 10 healthy volunteers at 1.5 T using NTE = 4 and NTE = 8 echoes. The separated images and maps were compared with a standard free-breathing electrocardiogram (ECG)-triggered acquisition. RESULTS: The method was validated in vivo, and physiological motion was resolved over all collected echoes. Across volunteers, PT provided respiratory and cardiac signals in agreement (r = 0.91 and r = 0.72) with SG of the first echo, and a higher correlation to the ECG (0.1% of missed triggers for PT vs. 5.9% for SG). The framework enabled pericardial fat imaging and quantification throughout the cardiac cycle, revealing a decrease in FF at end-systole by 11.4% ± 3.1% across volunteers (p < 0.0001). Motion-resolved end-diastolic 3D FF maps showed good correlation with ECG-triggered measurements (FF bias of -1.06%). A significant difference in free-running FF measured with NTE = 4 and NTE = 8 was found (p < 0.0001 in sub-cutaneous fat and p < 0.01 in pericardial fat). CONCLUSION: Free-running fat fraction mapping was validated at 1.5 T, enabling ME-GRE-based fat quantification with NTE = 8 echoes in 6:15 min.

Simulation of a virtual liver iron overload model and R2 * estimation using multispectral fat-water models for GRE and UTE acquisitions at 1.5 T and 3 T.

R2 *-MRI has emerged as a noninvasive alternative to liver biopsy for assessment of hepatic iron content (HIC). Multispectral fat-water R2 * modeling techniques such as the nonlinear least squares (NLSQ) fitting and autoregressive moving average (ARMA) models have been proposed for the accurate assessment of iron overload by also considering fat, which can otherwise confound R2 *-based HIC measurements in conditions of coexisting iron overload and steatosis. However, the R2 * estimation by these multispectral models has not been systematically investigated for various acquisition methods in iron overload only conditions and across the full clinically relevant range of HICs (0-40 mg Fe/g dry liver weight). The purpose of this study is to evaluate the R2 * accuracy and precision of multispectral models for various multiecho gradient echo (GRE) and ultrashort echo time (UTE) imaging acquisitions by constructing virtual iron overload models based on true histology and synthesizing MRI signals via Monte Carlo simulations at 1.5 T and 3 T, and comparing their results with monoexponential model and published in vivo R2 *-HIC calibrations. The signals were synthesized with TE1 = 1.0 ms for GRE and TE1 = 0.1 ms for UTE acquisition for varying echo spacing, ΔTE (0.1, 0.5, 1, 2 ms), and maximum echo time, TEmax (2, 4, 6, 10 ms). An iron-doped phantom study is also conducted to validate the simulation results in experimental GRE (TE1 = 1.2 ms, ΔTE = 0.72 ms, TEmax = 6.24 ms) and UTE (TE1 = 0.1 ms, ΔTE = 0.5 ms, TEmax = 6.1 ms) acquisitions. For GRE acquisitions, the multispectral ARMA and NLSQ models produced higher slopes (0.032-0.035) compared with the monoexponential model and published in vivo R2 *-HIC calibrations (0.025-0.028). However, for UTE acquisition for shorter echo spacing (≤0.5 ms) and longer maximum echo time, TEmax (≥6 ms), the multispectral and monoexponential signal models produced similar R2 *-HIC slopes (1.5 T, 0.028-0.032; 3 T, 0.014-0.016) and precision values (coefficient of variation < 25%) across the full clinical spectrum of HICs at both 1.5 T and 3 T. The phantom analysis also showed that all signal models demonstrated a significant improvement in R2 * estimation for UTE acquisition compared with GRE, confirming our simulation findings. Future work should investigate the performance of multispectral fat-water models by simulating liver models in coexisting conditions of iron overload and steatosis for accurate R2 * and fat quantification.

Imaging of traumatic mandibular fractures in young adults using CT-like MRI: a feasibility study.

OBJECTIVES: To assess and compare the diagnostic performance of CT-like images based on a three- dimensional (3D) T1-weighted spoiled gradient-echo sequence (3D T1 GRE) with CT in patients with acute traumatic fractures of the mandible. MATERIALS AND METHODS: Subjects with acute mandibular fractures diagnosed on conventional CT were prospectively recruited and received an additional 3 T MRI with a CT-like 3D T1 GRE sequence. The images were assessed by two radiologists with regard to fracture localization, degree of dislocation, and number of fragments. Bone to soft tissue contrast, diagnostic confidence, artifacts, and overall image quality were rated using a five-point Likert-scale. Agreement of measurements was assessed using an independent t-test. RESULTS: Fourteen subjects and 22 fracture sites were included (26 ± 3.9 years; 4 females, 10 males). All traumatic fractures were accurately detected on CT-like MRI (n = 22, κ 1.00 (95% CI 1.00-1.00)). There was no statistically significant difference in the assessment of the fracture dislocation (axial mean difference (MD) 0.06 mm, p = 0.93, coronal MD, 0.08 mm, p = 0.89 and sagittal MD, 0.04 mm, p = 0.96). The agreement for the fracture classification as well as the inter- and intra-rater agreement was excellent (range κ 0.92-0.98 (95% CI 0.96-0.99)). CONCLUSION: Assessment of mandibular fractures was feasible and accurate using CT-like MRI based on a 3D T1 GRE sequence and is comparable to conventional CT. CLINICAL RELEVANCE: For the assessment of acute mandibular fractures, CT-like MRI might become a useful alternative to CT in order to reduce radiation exposure particularly in young patients.

MRI of unruptured infectious intracranial aneurysms in infective endocarditis. A case-control study.

PURPOSE: To evaluate the usefulness of T2* and FLAIR sequences in the detection of unruptured infectious intracranial aneurysms (UIIAs) in infective endocarditis (IE) including the relationships between the lesion patterns within subarachnoid spaces and the presence of UIIA. METHODS: Retrospective review of 15 consecutive patients with definite IE undergoing MR imaging (FLAIR, T2*, DWI, CE-MRA, 3D-T1, CE-3DT1 sequences), in whom DSA detected infectious intracranial aneurysms (IIA). Aneurysmal features (diameter, location, morphology on DSA) and signal patterns onT2*, FLAIR and conventional MR sequences at the site of the UIIA, follow-up MRI and IE background, were analyzed. A control-group of 15 IE-patients without IIA at DSA served for comparison. RESULTS: Among 17 UIIAs studied, T2* sequence displayed a susceptibility vessel sign in 15/17 (88.2%), both distal and proximal, which matched with the IIA visualized on DSA. Three patterns of hyposignal areas were identified: (a) signet-ring or target-sign appearance (n = 7), (b) homogeneous, round-, oval- or pear-shaped area (n = 4), and (c) heterogeneous area (n = 4). A FLAIR hyperintensity of the lumen and of the adjacent cortex was present in 6 (35.3%) and 9 (53%) UIIAs, respectively. On T1 (12 UIIAs) a rounded hyposignal (n = 2), within the UIIA lumen matched with the FLAIR hypersignal. Using both T2* and FLAIR had an incremental value with 100% sensitivity and specificity. CONCLUSION: The susceptibility vessel sign is an MR imaging pattern frequently observed at the site of UIIAs in IE-patients. Both T2* and FLAIR may have the potential to depict UIIAs, regardless of their location and shape.

Towards in vivo ground truth susceptibility for single-orientation deep learning QSM: A multi-orientation gradient-echo MRI dataset.

Recently, deep neural networks have shown great potential for solving dipole inversion of quantitative susceptibility mapping (QSM) with improved results. However, these studies utilized their limited dataset for network training and inference, which may lead to untrustworthy conclusions. Thus, a common dataset is needed for a fair comparison between different QSM reconstruction networks. Additionally, finding an in vivo reference susceptibility map that matches acquired single-orientation phase data remains an open problem. Susceptibility tensor imaging (STI) χ33 and Calculation of Susceptibility through Multiple Orientation Sampling (COSMOS) are considered reference susceptibility candidates. However, a large number of multi-orientation GRE data for both STI and COSMOS reconstruction are now unavailable for training supervised neural networks for QSM. In this study, we reported the largest multi-orientation dataset, to the best of our knowledge in the QSM research field, with a total of 144 scans from 8 healthy subjects collected using a 3D GRE sequence from the same MR scanner. In addition, the parcellation of deep gray matter is also provided for automatically extracting susceptibility values. Five recently developed deep neural networks, i.e., xQSM, QSMnet, autoQSM, LPCNN, and MoDL-QSM were performed on this dataset. This potential data source could provide a common framework and labels to test the accuracy and robustness of deep neural networks for QSM reconstruction. This dataset has the potential to provide a benchmark of reference susceptibility for the deep learning-based QSM methods. Additionally, the trained COSMOS-labeled and χ33-labeled networks were tested on the pathological data to explore their potential applications. The data together with deep gray matter parcellation maps are now publicly available via an open repository at https://osf.io/yfms7/, and the raw multi-orientation GRE data are also available at https://osf.io/y6rc3/.

Gre factors prevent thermal and mechanical stresses induced by terahertz irradiation during transcription.

During transcription in cells, the transcription complex consisting of RNA polymerase, DNA and nascent RNA is exposed to fluctuating temperature and pressure. However, little is known about the mechanism of transcriptional homeostasis under fluctuating physical parameters. In this study, we generated these fluctuating parameters using pulsed local heating and acoustic waves in the reaction system of transcription by Escherichia coli RNA polymerase, using a terahertz free-electron laser. We demonstrated that transcription processes, including abortive initiation and elongation pausing, and the fidelity of elongation are significantly affected by the laser-based local perturbations. We also found that all these functional alternations in the transcription process are almost completely mitigated by the presence of Gre proteins. It is well known that Gre proteins enhance RNA cleavage of polymerase by binding to the pore structure termed secondary channel. Recently, the chaperone activities have also been proposed for Gre proteins, yet the details directly associated with transcription are largely unknown. Our finding indicates that Gre proteins are necessary for maintaining transcriptional homeostasis under thermal and mechanical stresses.

MULTI-parametric MR imaging with fLEXible design (MULTIPLEX).

PURPOSE: To introduce a gradient echo (GRE) -based method, namely MULTIPLEX, for single-scan 3D multi-parametric MRI with high resolution, signal-to-noise ratio (SNR), accuracy, efficiency, and acquisition flexibility. THEORY: With a comprehensive design with dual-repetition time (TR), dual flip angle (FA), multi-echo, and optional flow modulation features, the MULTIPLEX signals contain information on radiofrequency (RF) B1t fields, proton density, T1 , susceptibility and blood flows, facilitating multiple qualitative images and parametric maps. METHODS: MULTIPLEX was evaluated on system phantom and human brains, via visual inspection for image contrasts and quality or quantitative evaluation via simulation, phantom scans and literature comparison. Region-of-interest (ROI) analysis was performed on parametric maps of the system phantom and brain scans, extracting the mean and SD of the T1 , T2∗ , proton density (PD), and/or quantitative susceptibility mapping (QSM) values for comparison with reference values or literature. RESULTS: One MULTIPLEX scan offers multiple sets of images, including but not limited to: composited PDW/T1 W/ T2∗ W, aT1 W, SWI, MRA (optional), B1t map, T1 map, T2∗ / R2∗ maps, PD map, and QSM. The quantitative error of phantom T1 , T2∗ and PD mapping were <5%, and those in brain scans were in good agreement with literature. MULTIPLEX scan times for high resolution (0.68 × 0.68 × 2 mm3 ) whole brain coverage were about 7.5 min, while processing times were <1 min. With flow modulation, additional MRA images can be obtained without affecting the quality or accuracy of other images. CONCLUSION: The proposed MUTLIPLEX method possesses great potential for multi-parametric MR imaging.

Augmented T1 -weighted steady state magnetic resonance imaging.

T1 contrasts obtained using short-TR incoherent steady state gradient echo (GRE) methods are generally suboptimal, to which non-T1 factors in the signals play a major part. In this work, we proposed an augmented T1 -weighted (aT1 W) method to extract the signal ratio between routine GRE T1 W and proton density-weighted signals that effectively removes the non-T1 effects from the original T1 W signals, including proton density, T2 * decay, and coil sensitivity. A recently proposed multidimensional integration (MDI) technique was incorporated in the aT1 W calculation for better signal-to-noise ratio (SNR) performance. For comparison between aT1 W and T1 W results, Monte Carlo noise analysis was performed via simulation and on scanned data, and region-of-interest (ROI) analysis and comparison was performed on the system phantom. For brain scans, the image contrast, noise behavior, and SNR of aT1 W images were compared with routine GRE and inversion-recovery-based T1 W images. The proposed aT1 W method yielded saliently improved T1 contrasts (potentially > 30% higher contrast-to-noise ratio [CNR]) than routine GRE T1 W images. Good spatial homogeneity and signal consistency as well as high SNR/CNR were achieved in aT1 W images using the MDI technique. For contrast-enhanced (CE) imaging, aT1 W offered stronger post-CE contrast and better boundary delineation than T1 MPRAGE images while using a shorter scan time.

Efficient phase-cycling strategy for high-resolution 3D gradient-echo quantitative parameter mapping.

Magnetization-prepared (MP) gradient-echo (GRE) sequences suffer from signal contaminations from T1 recovery during the readout train, which can be eliminated by paired RF phase cycling (PC) at the cost of doubling the scan time. The objective of this study was to develop and validate a novel unpaired PC strategy to eliminate the time penalty for high-resolution quantitative parameter mapping in 3D MP-GRE sequences. Based on the observation that the contaminating T1 recovery signal along the GRE readout train is independent of magnetization preparation, its impact can be eliminated using a novel curve-fitting approach with complex-valued data without needing paired PC acquisitions. Four new unpaired PC schemes were compared with two traditional paired PC schemes in both phantom and in vivo human knee studies at 3 T using a MP angle-modulated partitioned k-space spoiled gradient-echo snapshots (MAPSS) T1ρ mapping sequence. In the phantom study, all methods resulted in consistent T1ρ measurements (∆T1ρ < 0.5%) at the center slice when B0 /B1 values were uniform. Results were not consistent when off-center slices with nonideal B0 /B1 were included. Two unpaired PC schemes had comparable or significantly improved quantitative accuracy and scan-rescan reproducibility compared with the paired PC schemes. There was no significant T1ρ quantitative variability increase or spatial fidelity loss using the new unpaired PC schemes. Unpaired PC schemes also had different T1ρ spectral responses at different B0 frequency offsets, which can potentially be exploited to reduce sensitivity to B0 field inhomogeneities. The human knee study results were consistent with the phantom study findings. In conclusion, an unpaired PC strategy potentially allows more accurate quantitative parameter mapping with halved scan time compared with the paired PC approach to eliminate signal contaminations from T1 recovery. It therefore offers additional flexibility in SNR optimization, spatial resolution improvement, and choice of imaging sampling points to obtain more accurate quantitative parameter mapping.

Predicting Academic Difficulty in Veterinary Medicine: A Case-Control Study.

A veterinary education is costly and time-consuming, so it is in the best interests of applicants and colleges alike that admissions processes be fair and select applicants who are likely to succeed. We employed a case-control study to explore whether any of 28 admissions variables used by a veterinary college located in the Midwest region of the United States predicted which students would encounter academic difficulty in the veterinary curriculum. Participants were selected from the veterinary classes admitted between 2008 and 2017. We defined academic difficulty cases (n = 55) as any students dismissed from the program or placed on academic probation. Controls (n = 220) were selected at random from the same classes, excluding the academic difficulty cases, students with honor code violations, or any who had exited the program early for any reason other than participation in a concurrent program. Admissions variables included gender, citizenship, underrepresented status, state of residence, age, interview scores, GPA (science), GRE scores, undergraduate credits, participation in honors courses, community college credits, repeats/withdrawals of required undergraduate courses, course load, and admissions committee review criteria including work experience, animal/vet experience, references, essays, leadership, personal development, special circumstances, and overall committee score. Zero-order correlations for academic difficulty were significant for underrepresented status, age, GPA (science), verbal and quantitative GRE scores, repeats/withdrawals, and references. When combined in logistic regression, only science GPA, verbal GRE, and references significantly and independently predicted struggler status.