Increase Acquisition Efficiency Research Articles

Quick Estimation of Minimum Hearing Levels Using a Binaural Multifrequency Stimulus Paradigm: Proof of Concept.

Objective estimation of minimum hearing levels using auditory brainstem responses (ABRs) elicited by single frequency tone-bursts presented monaurally is currently considered the gold standard. However, the data acquisition time to estimate thresholds (for both ears across four audiometric frequencies) using this method usually exceeds the sleep time (ranging between 35 and 49 minutes) in infants below 4 months, thus providing incomplete information of hearing status which in turn delays timely clinical intervention. Alternate approaches using faster rate, or tone-burst trains have not been readily accepted due to additional hardware and software requirements. We propose here a novel binaural multifrequency stimulation paradigm wherein several stimuli of different frequencies are presented binaurally in an interleaved manner. The rationale here is that the proposed paradigm will increase acquisition efficiency, significantly reduce test time, and improve accuracy by incorporating an automatic wave V detection algorithm. It is important to note that this paradigm can be easily implemented in most commercial ABR systems currently used by most clinicians. Using this binaural multifrequency paradigm, ear specific ABRs were recorded in 30 normal-hearing young adults to both tone-bursts, and narrow-band (NB) iChirps at 500, 1000, 2000, and 4000 Hz. Comparison of ABRs elicited by tone-bursts and narrow-band chirps allowed us to determine if NB iChirps elicited a more robust wave V component compared with the tone-bursts. ABR data were characterized by measures of minimum hearing levels; wave V amplitude; and response detectability for two electrode configurations (high forehead-C7; and high forehead-linked mastoids). Consistent with the research literature, wave V response amplitudes were relatively more robust for NB iChirp stimuli compared with tone-burst stimuli. The easier identification and better detectability of wave V for the NB iChirps at lower stimulus levels contributed to their better thresholds compared with tone-burst elicited responses. It is important to note that binaural multifrequency hearing levels close to minimum hearing levels were determined in approximately 22 minutes using this paradigm-appreciably quicker than the 45 to 60 minutes or longer time required for threshold determination using the conventional single frequency method. Our novel and simple paradigm using either NB iChirps or tone-bursts provides a reliable method to rapidly estimate the minimum hearing levels across audiometric frequencies for both ears. Incorporation of an automatic wave V detection algorithm increases objectivity and further reduce test time and facilitate early hearing identification and intervention.

Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification and Compartment and Process Coverage and Enables More Reflective Protein-Level Label-Free Quantitation.

The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement, with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Herein, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition methods. Analysis of offline fractionated cell line digests using both separations revealed an increase in peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. RAW proteomic data have been uploaded to the MassIVE repository with the primary accession code MSV000091495.

Concomitant field compensation of spiral turbo spin-echo at 0.55T.

Diagnostic-quality neuroimaging methods are vital for widespread clinical adoption of low field MRI. Spiral imaging is an efficient acquisition method that can mitigate the reduced signal-to-noise ratio at lower field strengths. As concomitant field artifacts are worse at lower field, we propose a generalizable quadratic gradient-field nulling as an echo-to-echo compensation and apply it to spiral TSE at 0.55T. A spiral in-out TSE acquisition was developed with a compensation for concomitant field variation between spiral interleaves, by adding bipolar gradients around each readout to minimize phase differences at each refocusing pulse. Simulations were performed to characterize concomitant field compensation approaches. We demonstrate our proposed compensation method in phantoms and (n = 8) healthy volunteers at 0.55T. Spiral read-outs with integrated spoiling demonstrated strong concomitant field artifacts but were mitigated using the echo-to-echo compensation. Simulations predicted a decrease of concomitant field phase RMSE between echoes of 42% using the proposed compensation. Spiral TSE improved SNR by 17.2 ± 2.3% compared to reference Cartesian acquisition. We demonstrated a generalizable approach to mitigate concomitant field artifacts for spiral TSE acquisitions via the addition of quadratic-nulling gradients, which can potentially improve neuroimaging at low-field through increased acquisition efficiency.

Reconstruction for 7T high-resolution whole-brain diffusion MRI using two-stage N/2 ghost correction and L1-SPIRiT without single-band reference.

To combine a new two-stage N/2 ghost correction and an adapted L1-SPIRiT method for reconstruction of 7T highly accelerated whole-brain diffusion MRI (dMRI) using only autocalibration scans (ACS) without the need of additional single-band reference (SBref) scans. The proposed ghost correction consisted of a 3-line reference approach in stage 1 and the reference-free entropy method in stage 2. The adapted L1-SPIRiT method was formulated within the 3D k-space framework. Its efficacy was examined by acquiring two dMRI data sets at 1.05-mm isotropic resolutions with a total acceleration of 6 or 9 (i.e., 2-fold or 3-fold slice and 3-fold in-plane acceleration). Diffusion analysis was performed to derive DTI metrics and estimate fiber orientation distribution functions (fODFs). The results were compared with those of 3D k-space GRAPPA using only ACS, all in reference to 3D k-space GRAPPA using both ACS and SBref (serving as a reference). The proposed ghost correction eliminated artifacts more robustly than conventional approaches. Our adapted L1-SPIRiT method outperformed 3D k-space GRAPPA when using only ACS, improving image quality to what was achievable with 3D k-space GRAPPA using both ACS and SBref scans. The improvement in image quality further resulted in an improvement in estimation performances for DTI and fODFs. The combination of our new ghost correction and adapted L1-SPIRiT method can reliably reconstruct 7T highly accelerated whole-brain dMRI without the need of SBref scans, increasing acquisition efficiency and reducing motion sensitivity.

Single photon lidar signal attenuation under boreal forest conditions

ABSTRACT Single-photon lidar (SPL100) is a recently commercialized airborne lidar system facilitating efficient wide-area acquisitions of high-density point clouds due to its capacity for higher altitude acquisitions compared to traditional linear-mode lidar (LML) systems. Increased acquisition efficiency and point densities make SPL100 attractive for forest management applications. SPL100 utilizes 532 nm (green wavelength) lasers, wherein there is reduced reflectance from vegetation, increased sensitivity to solar noise, and increased signal attenuation, which may impact the vertical distribution of SPL100 returns in forest canopies. We assessed SPL100 data acquisitions over managed forests in north-eastern Ontario, Canada, using high-density unmanned aerial vehicle-borne laser scanning (ULS) data as reference over a range of forest conditions with variable vertical structure. Signal attenuation depth of individual SPL100 returns was estimated through a surface model normalization approach stratified by a ULS-derived structural index that compared densities of returns in the upper canopy to low vegetation and near ground. Canopy signal attenuation was closely matched in both systems, particularly in the upper canopy and near the ground surface; however, results showed a 31% reduction in the relative characterization of mid-canopy vegetation layers by SPL100 under conditions identified by the structural index as closed canopy, compared to the ULS system.

Rapid and efficient generation of T-cell receptor-like antibodies using chip-based single-cell analysis.

Generation of TCR-like monoclonal antibodies using conventional methods is markedly laborious and inefficient. We have proposed improvements of ISAAC (chip-based Ab-secreting cell [ASC] screening method), allows comprehensive analysis of ASCs at the single-cell level to obtain TCR-like antibodies; blocking procedure enables us to avoid the detection of non-TCR-like antibodies.

Common Information Enhanced Reconstruction for Accelerated High-resolution Multi-shot Diffusion Imaging

PurposeMulti-shot technique can effectively achieve high-resolution diffusion weighted images, but the acquisition time of multi-shot technique is prolonged, especially for multiple direction diffusion encoding. Thus, increasing acquisition efficiency is highly desirable for high-resolution diffusion tensor imaging (DTI). In this study, based on the assumption that different diffusion directions share the common information, image ratio constrained reconstruction (IRCR) combined with iterative self-consistent parallel imaging reconstruction (SPIRiT) is proposed to improve data sampling efficiency and image reconstruction fidelity for high-resolution DTI. Theory and methodsThe proposed reconstruction framework is named Common Information Enhanced Reconstruction (CIER). Inter-image correlation among different direction diffusion-weighted images is used through common information, which is an isotropic component and structure, for improving the performance of reconstruction. The framework consists of three steps. (i) Pre-processing: three intermediate multi-shot images, low-resolution composite image, high-resolution composite image and low-resolution diffusion weighted image, are generated based on the SPIRiT method. (ii) IRCR: the initial high–resolution diffusion weighted image is calculated from the images in step (i) based on that the ratio map between high-resolution images is approximated by the ratio map between the corresponding low-resolution images. (iii) Final SPIRiT reconstruction: the final image is generated with the image from IRCR as initialization by considering data consistency only in the SPIRiT calculation. A specific implementation based on multishot variable density spiral (VDS) DTI is used to demonstrate the method. ResultsThe proposed CIER method was compared with the traditional reconstruction methods, conjugate gradient SENSE (CG-SENSE), L1-regularized SPIRiT (L1-SPIRiT), and anisotropic-sparsity SPIRiT (AS-SPIRiT) in brain DTI at acceleration factors of 3 to 7. CIER provided better diffusion image quality than other methods shown by both qualitative and quantitative results, especially at higher undersampling acceleration factors. ConclusionCIER offers better diffusion image quality at higher undersampling acceleration factors for high-resolution DTI. Both qualitative and quantitative results prove that common information can be used to improve sampling efficiency and maintain the image quality of diffusion-weighted images.

The Galperin source: A novel efficient multicomponent seismic source

Multicomponent acquisition enables a more complete observation of the seismic wavefield compared with single-component measurements and has therefore experienced increased interest in the past few decades. Whereas the use of multicomponent receivers is well-established, efficient and effective multicomponent sources are still difficult to realize. One of the main drawbacks of common multicomponent sources is that the source coupling differs for different components. Differences in the source coupling can lead to amplitude variations introducing uncertainties when jointly analyzing data from two or three components (e.g., for multicomponent polarization analysis). To overcome this problem, we have designed a new multicomponent vector source, referred to as the Galperin source. The design is inspired by the Galperin receiver configuration, and it consists of three orthogonal source vectors ([Formula: see text], [Formula: see text], and [Formula: see text]), which all have the same inclination relative to the horizontal. Using the Galperin configuration, three orthogonal source components can be acquired without moving the source and changing the source coupling, which also increases acquisition efficiency. We built a prototype of the Galperin source and compared it with other multicomponent sources used for near-surface investigations. Comparisons in the time and frequency domains indicate a good agreement between data acquired using the Galperin source and other, more conventional, sources. However, because the three source acquisition vectors [Formula: see text], [Formula: see text], and [Formula: see text] and the resulting processing coordinates [Formula: see text], [Formula: see text], and [Formula: see text] are linked by a rotational matrix, errors on one component can project into others. Therefore, precise leveling of the Galperin source and identical source strength for all three source components is essential to minimize errors.

Parallel imaging and compressed sensing combined framework for accelerating high-resolution diffusion tensor imaging using inter-image correlation.

Increasing acquisition efficiency is always a challenge in high-resolution diffusion tensor imaging (DTI), which has low signal-to-noise ratio and is sensitive to reconstruction artifacts. In this study, a parallel imaging (PI) and compressed sensing (CS) combined framework is proposed, which features motion error correction, PI calibration, and sparsity model using inter-image correlation tailored for high-resolution DTI. The proposed method, named anisotropic sparsity SPIRiT, consists of three steps: (i) motion-induced phase error estimation, (ii) initial CS reconstruction and PI kernel calibration, and (iii) final reconstruction combining PI and CS. Inter-image correlation of diffusion-weighted images are used through anisotropic signals for improved sparsity. A specific implementation based on multishot variable density spiral DTI is used to demonstrate the method. The proposed reconstruction method was compared with CG-SENSE, CS-based joint reconstruction, and PI and CS combined methods with L1 and joint sparsity regularization, in brain DTI experiments at acceleration factors of 3 to 5. Both qualitative and quantitative results demonstrated that the proposed method resulted in better preserved image quality and more accurate DTI parameters than other methods. The proposed method can accelerate high-resolution DTI acquisition effectively by using the sharable information among different diffusion encoding directions.

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins constitute a recently identified prokaryotic defense system against invading nucleic acids. DNA segments, termed protospacers, are integrated into the CRISPR array in a process called adaptation. Here, we establish a PCR-based assay that enables evaluating the adaptation efficiency of specific spacers into the type I-E Escherichia coli CRISPR array. Using this assay, we provide direct evidence that the protospacer adjacent motif along with the first base of the protospacer (5'-AAG) partially affect the efficiency of spacer acquisition. Remarkably, we identified a unique dinucleotide, 5'-AA, positioned at the 3' end of the spacer, that enhances efficiency of the spacer's acquisition. Insertion of this dinucleotide increased acquisition efficiency of two different spacers. DNA sequencing of newly adapted CRISPR arrays revealed that the position of the newly identified motif with respect to the 5'-AAG is important for affecting acquisition efficiency. Analysis of approximately 1 million spacers showed that this motif is overrepresented in frequently acquired spacers compared with those acquired rarely. Our results represent an example of a short nonprotospacer adjacent motif sequence that affects acquisition efficiency and suggest that other as yet unknown motifs affect acquisition efficiency in other CRISPR systems as well.

High efficiency multishot interleaved spiral‐in/out: Acquisition for high‐resolution BOLD fMRI

Growing demand for high spatial resolution blood oxygenation level dependent (BOLD) functional magnetic resonance imaging faces a challenge of the spatial resolution versus coverage or temporal resolution tradeoff, which can be addressed by methods that afford increased acquisition efficiency. Spiral acquisition trajectories have been shown to be superior to currently prevalent echo-planar imaging in terms of acquisition efficiency, and high spatial resolution can be achieved by employing multiple-shot spiral acquisition. The interleaved spiral in/out trajectory is preferred over spiral-in due to increased BOLD signal contrast-to-noise ratio (CNR) and higher acquisition efficiency than that of spiral-out or noninterleaved spiral in/out trajectories (Law & Glover. Magn Reson Med 2009; 62:829-834.), but to date applicability of the multishot interleaved spiral in/out for high spatial resolution imaging has not been studied. Herein we propose multishot interleaved spiral in/out acquisition and investigate its applicability for high spatial resolution BOLD functional magnetic resonance imaging. Images reconstructed from interleaved spiral-in and -out trajectories possess artifacts caused by differences in T2 decay, off-resonance, and k-space errors associated with the two trajectories. We analyze the associated errors and demonstrate that application of conjugate phase reconstruction and spectral filtering can substantially mitigate these image artifacts. After applying these processing steps, the multishot interleaved spiral in/out pulse sequence yields high BOLD CNR images at in-plane resolution below 1 × 1 mm while preserving acceptable temporal resolution (4 s) and brain coverage (15 slices of 2 mm thickness). Moreover, this method yields sufficient BOLD CNR at 1.5 mm isotropic resolution for detection of activation in hippocampus associated with cognitive tasks (Stern memory task). The multishot interleaved spiral in/out acquisition is a promising technique for high spatial resolution BOLD functional magnetic resonance imaging applications.

Barley Root Growth and Phosphorus Bioavailability in Soil Treated with Phosphate Rocks

The effects of five phosphate rocks (originating from Algeria, northern Florida, North Carolina, Senegal, and Morocco) with various phosphorus (P) solubilities on P bioavailability, root growth, and P uptake of spring barley crops were studied on an acidic sandy soil in microlysimeters, in a pot experiment and by dynamic simulation. Root length and P influx varied significantly, influenced by the P and calcium carbonate (CaCO3) content and reactivity of the P sources. Phosphate rock (PR) treatments enhanced root growth. The simulation results demonstrated the contribution of root hair formation and P mobilization by rhizosphere acidification in the increased acquisition efficiency of barley in PR‐treated soil.

Myocardial tagging with SSFP.

This work presents the first implementation of myocardial tagging with refocused steady-state free precession (SSFP) and magnetization preparation. The combination of myocardial tagging (a noninvasive method for quantitative measurement of regional and global cardiac function) with the high tissue signal-to-noise ratio (SNR) obtained with SSFP is shown to yield improvements in terms of the myocardium-tag contrast-to-noise ratio (CNR) and tag persistence when compared to the current standard fast gradient-echo (FGRE) tagging protocol. Myocardium-tag CNR and tag persistence were studied using numerical simulations as well as phantom and human experiments. Both quantities were found to decrease with increasing imaging flip angle (alpha) due to an increased tag decay rate and a decrease in myocardial steady-state signal. However, higher alpha yielded better blood-myocardium contrast, indicating that optimal alpha is dependent on the application: higher alpha for better blood-myocardium boundary visualization, and lower alpha for better tag persistence. SSFP tagging provided the same myocardium-tag CNR as FGRE tagging when acquired at four times the bandwidth and better tag- and blood-myocardium CNRs than FGRE tagging when acquired at equal or twice the receiver bandwidth (RBW). The increased acquisition efficiency of SSFP allowed decreases in breath-hold duration, or increases in temporal resolution, as compared to FGRE.

Use of multicoil arrays for separation of signal from multiple slices simultaneously excited.

Increased acquisition efficiency has been achieved by exciting several slices simultaneously. The mixed data were unfolded to produce separate slices using the spatial encoding information inherent in a multicoil receiver system. Each coil yields a linear combination of signals from all excited slices weighted by the sensitivity of each coil. A matrix inversion provides a solution to unfold these images.