Sample-centred shimming enables independent parallel NMR detection
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ABSTRACT:
SUBMITTER: Cheng Y
PROVIDER: S-EPMC9389490 | biostudies-literature | 2022 Jan
REPOSITORIES: biostudies-literature
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Project description:PurposeTo develop a new concept for a hardware platform that enables integrated parallel reception, excitation, and shimming.TheoryThis concept uses a single coil array rather than separate arrays for parallel excitation/reception and B0 shimming. It relies on a novel design that allows a radiofrequency current (for excitation/reception) and a direct current (for B0 shimming) to coexist independently in the same coil.MethodsProof-of-concept B0 shimming experiments were performed with a two-coil array in a phantom, whereas B0 shimming simulations were performed with a 48-coil array in the human brain.ResultsOur experiments show that individually optimized direct currents applied in each coil can reduce the B0 root-mean-square error by 62-81% and minimize distortions in echo-planar images. The simulations show that dynamic shimming with the 48-coil integrated parallel reception, excitation, and shimming array can reduce the B0 root-mean-square error in the prefrontal and temporal regions by 66-79% as compared with static second-order spherical harmonic shimming and by 12-23% as compared with dynamic shimming with a 48-coil conventional shim array.ConclusionOur results demonstrate the feasibility of the integrated parallel reception, excitation, and shimming concept to perform parallel excitation/reception and B0 shimming with a unified coil system as well as its promise for in vivo applications.
| S-EPMC3800110 | biostudies-literature
Project description:Rapid drug development requires a high throughput screening technology. NMR could benefit from parallel detection but is hampered by technical obstacles. Detection sites must be magnetically shimmed to ppb uniformity, which for parallel detection is precluded by commercial shimming technology. Here we show that, by centering a separate shim system over each detector and employing deep learning to cope with overlapping non-orthogonal shimming fields, parallel detectors can be rapidly calibrated. Our implementation also reports the smallest NMR stripline detectors to date, based on an origami technique, facilitating further upscaling in the number of detection sites within the magnet bore.
| S-EPMC10589267 | biostudies-literature
Project description:A novel approach for automated high throughput NMR spectroscopy with improved mass-sensitivity is accomplished by integrating microfluidic technologies and micro-NMR resonators. A flow system is utilized to transport a sample of interest from outside the NMR magnet through the NMR detector, circumventing the relatively vast dead volume in the supplying tube by loading a series of individual sample plugs separated by an immiscible fluid. This dual-phase flow demands a real-time robust sensing system to track the sample position and velocities and synchronize the NMR acquisition. In this contribution, we describe an NMR probe head that possesses a microfluidic system featuring: (i) a micro saddle coil for NMR spectroscopy and (ii) a pair of interdigitated capacitive sensors flanking the NMR detector for continuous position and velocity monitoring of the plugs with respect to the NMR detector. The system was successfully tested for automating flow-based measurement in a 500 MHz NMR system, enabling high resolution spectroscopy and NMR sensitivity of 2.18 nmol s1/2 with the flow sensors in operation. The flow sensors featured sensitivity to an absolute difference of 0.2 in relative permittivity, enabling distinction between most common solvents. It was demonstrated that a fully automated NMR measurement of nine individual 120 μL samples could be done within 3.6 min or effectively 15.3 s per sample.
| S-EPMC8433180 | biostudies-literature
Project description:PurposeIntegrated parallel reception, excitation, and shimming (iPRES) coil arrays allow radio-frequency currents and direct currents to flow in the same coils, which enables excitation/reception and localized B0 shimming with a single coil array. The purpose of this work was to improve their shimming performance by adding the capability to shim higher-order local B0 inhomogeneities that are smaller than the radio-frequency coil elements.MethodsA novel design was proposed in which each radio-frequency/shim coil element is divided into multiple direct current loops, each using an independent direct current current, to increase the number of magnetic fields available for shimming while maintaining the signal-to-noise ratio of the coil. This new design is termed iPRES(N), where N represents the number of direct current loops per radio-frequency coil element. Proof-of-concept phantom and human experiments were performed with an 8-channel body coil array to demonstrate its advantages over the original iPRES(1) design.ResultsThe average B0 homogeneity in various organs before shimming and after shimming with the iPRES(1) or iPRES(3) coil arrays was 0.24, 0.11, and 0.05 ppm, respectively. iPRES(3) thus reduced the B0 inhomogeneity by 53% and further reduced distortions in echo-planar images of the abdomen when compared with iPRES(1).ConclusioniPRES(N) can correct for localized B0 inhomogeneities more effectively than iPRES(1) with no signal-to-noise ratio loss, resulting in a significant improvement in image quality. Magn Reson Med 77:2077-2086, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
| S-EPMC5107366 | biostudies-literature
Project description:PurposeIntegrated parallel reception, excitation, and shimming coil arrays with N shim loops per radio-frequency (RF) coil element (iPRES(N)) allow an RF current and N direct currents (DC) to flow in each coil element, enabling simultaneous reception/excitation and shimming of highly localized B0 inhomogeneities. The purpose of this work was to reduce the cost and complexity of this design by reducing the number of DC power supplies required by a factor N, while maintaining a high RF and shimming performance.MethodsIn the proposed design, termed adaptive iPRES(N) (iPRES(N)-A), each coil element only requires one DC power supply, but uses microelectromechanical systems switches to adaptively distribute the DC current into the appropriate shim loops to generate the desired magnetic field for B0 shimming. Proof-of-concept phantom experiments with an iPRES(2)-A coil and simulations in the human abdomen with an 8-channel iPRES(4)-A body coil array were performed to demonstrate the advantages of this innovative design.ResultsThe iPRES(2)-A coil showed no loss in signal-to-noise ratio and provided a much more effective correction of highly localized B0 inhomogeneities and geometric distortions than an equivalent iPRES(1) coil (88.2% vs. 32.2% lower B0 root-mean-square error). The iPRES(4)-A coil array showed a comparable shimming performance as that of an equivalent iPRES(4) coil array (52.6% vs. 54.2% lower B0 root-mean-square error), while only requiring 8 instead of 32 power supplies.ConclusionThe iPRES(N)-A design retains the ability of the iPRES(N) design to shim highly localized B0 inhomogeneities, while drastically reducing its cost and complexity. Magn Reson Med 80:371-379, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
| S-EPMC5876104 | biostudies-literature
Project description:High-throughput data-independent acquisition (DIA) is the method of choice for quantitative proteomics, combining the best practices of targeted and shotgun approaches. The resultant DIA spectra are, however, highly convolved and with no direct precursor-fragment correspondence, complicating biological sample analysis. Here, we present CANDIA (canonical decomposition of data-independent-acquired spectra), a GPU-powered unsupervised multiway factor analysis framework that deconvolves multispectral scans to individual analyte spectra, chromatographic profiles, and sample abundances, using parallel factor analysis. The deconvolved spectra can be annotated with traditional database search engines or used as high-quality input for de novo sequencing methods. We demonstrate that spectral libraries generated with CANDIA substantially reduce the false discovery rate underlying the validation of spectral quantification. CANDIA covers up to 33 times more total ion current than library-based approaches, which typically use less than 5% of total recorded ions, thus allowing quantification and identification of signals from unexplored DIA spectra.
| S-EPMC7733873 | biostudies-literature
Project description:PurposeTo optimize pseudo-continuous arterial spin labeling (pCASL) for 7 T, and to further improve the labeling efficiency with parallel RF transmission transmit B1 ( B1+ ) shimming.MethodspCASL parameters were optimized based on B1+/B0 field distributions at 7 T with simulation. To increase labeling efficiency, the B1+ amplitude at inflowing arteries was increased with parallel RF transmission B1+ shimming. The "indv-shim" with shimming weights calculated for each individual subject, and the "univ-shim" with universal weights calculated on a group of 12 subjects, were compared with circular polarized (CP) shim. The optimized pCASL sequences with three B1+ shimming modes (indv-shim, univ-shim, and CP-shim) were evaluated in 6 subjects who underwent two repeated scans 24 hours apart, along with a pulsed ASL sequence. Quantitative metrics including mean B1+ amplitude, perfusion, and intraclass correlation coefficient were calculated. The optimized 7T pCASL was compared with standard 3T pCASL on 5 subjects, using spatial SNR and temporal SNR.ResultsThe optimal pCASL parameter set (RF duration/gap = 300/250 us, Gave=0.6mT/m,gRatio=10 ) achieved robust perfusion measurement in the presence of B1+/B0 inhomogeneities. Both indv-shim and univ-shim significantly increased B1+ amplitude compared with CP-shim in simulation and in vivo experiment (P < .01). Compared with CP-shim, perfusion signal was increased by 9.5% with indv-shim (P < .05) and by 5.3% with univ-shim (P = .35). All three pCASL sequences achieved fair to good repeatability (intraclass correlation coefficient ≥ 0.5). Compared with 3T pCASL, the optimized 7T pCASL achieved 78.3% higher spatial SNR and 200% higher temporal SNR.ConclusionThe optimized pCASL achieved robust perfusion imaging at 7 T, while both indv-shim and univ-shim further increased labeling efficiency.
| S-EPMC8616784 | biostudies-literature
Project description:Bioacoustic research spans a wide range of biological questions and applications, relying on identification of target species or smaller acoustic units, such as distinct call types. However, manually identifying the signal of interest is time-intensive, error-prone, and becomes unfeasible with large data volumes. Therefore, machine-driven algorithms are increasingly applied to various bioacoustic signal identification challenges. Nevertheless, biologists still have major difficulties trying to transfer existing animal- and/or scenario-related machine learning approaches to their specific animal datasets and scientific questions. This study presents an animal-independent, open-source deep learning framework, along with a detailed user guide. Three signal identification tasks, commonly encountered in bioacoustics research, were investigated: (1) target signal vs. background noise detection, (2) species classification, and (3) call type categorization. ANIMAL-SPOT successfully segmented human-annotated target signals in data volumes representing 10 distinct animal species and 1 additional genus, resulting in a mean test accuracy of 97.9%, together with an average area under the ROC curve (AUC) of 95.9%, when predicting on unseen recordings. Moreover, an average segmentation accuracy and F1-score of 95.4% was achieved on the publicly available BirdVox-Full-Night data corpus. In addition, multi-class species and call type classification resulted in 96.6% and 92.7% accuracy on unseen test data, as well as 95.2% and 88.4% regarding previous animal-specific machine-based detection excerpts. Furthermore, an Unweighted Average Recall (UAR) of 89.3% outperformed the multi-species classification baseline system of the ComParE 2021 Primate Sub-Challenge. Besides animal independence, ANIMAL-SPOT does not rely on expert knowledge or special computing resources, thereby making deep-learning-based bioacoustic signal identification accessible to a broad audience.
| S-EPMC9763499 | biostudies-literature
Project description:PurposeA ratio adjustable power splitter (RAPS) circuit was recently proposed for add-on RF shimming and array-compressed parallel transmission. Here we propose a new RAPS circuit design based on off-the-shelf components for improved performance and manufacturability.Theory and methodsThe original RAPS used a pair of home-built Wilkinson splitter and hybrid coupler connected by a pair of connectorized coaxial cables. Here we propose a new hybrid-pair RAPS (or HP-RAPS) circuit that replaces the home-built circuits with two commercially available hybrid couplers and replaces connectorized cables with interchangeable microstrip lines. We derive the relation between the desired splitting ratio and the required phase shifts for HP-RAPS and investigate how to generate arbitrary splitting ratios using paired meandering and straight lines. Several HP-RAPSs with different splitting ratios were fabricated and tested on the workbench and MRI experiments.ResultsThe splitting ratio of an HP-RAPS circuit has a tan or cot dependence on the meandering line's additional length compared to the straight line. The fabricated HP-RAPSs exhibit accurate splitting ratios as expected (<4% deviations) and generate transmit fields that well agree with predicted fields. They also demonstrated a low insertion loss of 0.33 dB, high output isolation of -26 dB, and acceptable impedance matching of -16 dB.ConclusionA novel HP-RAPS circuit was developed and implemented. It is easy-to-fabricate/reproduce with minimal expertise. It also preserves the features of the original RAPS circuit (ratio-adjustable, small footprint, etc.) with lower insertion loss.
| S-EPMC8568636 | biostudies-literature
Project description:Most severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests have relied on RNA extraction followed by reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays. Whereas automation improved logistics and different pooling strategies increased testing capacity, highly multiplexed next-generation sequencing (NGS) diagnostics remain a largely untapped resource. NGS tests have the potential to markedly increase throughput while providing crucial SARS-CoV-2 variant information. Current NGS-based detection and genotyping assays for SARS-CoV-2 are costly, mostly due to parallel sample processing through multiple steps. Here, we have established ApharSeq, in which samples are barcoded in the lysis buffer and pooled before reverse transcription. We validated this assay by applying ApharSeq to more than 500 clinical samples from the Clinical Virology Laboratory at Hadassah hospital in a robotic workflow. The assay was linear across five orders of magnitude, and the limit of detection was Ct 33 (~1000 copies/ml, 95% sensitivity) with >99.5% specificity. ApharSeq provided targeted high-confidence genotype information due to unique molecular identifiers incorporated into this method. Because of early pooling, we were able to estimate a 10- to 100-fold reduction in labor, automated liquid handling, and reagent requirements in high-throughput settings compared to current testing methods. The protocol can be tailored to assay other host or pathogen RNA targets simultaneously. These results suggest that ApharSeq can be a promising tool for current and future mass diagnostic challenges.
| S-EPMC9928115 | biostudies-literature