Highly-accelerated CEST MRI using frequency-offset-dependent k-space sampling and deep-learning reconstruction.

PURPOSE: To develop a highly accelerated CEST Z-spectral acquisition method using a specifically-designed k-space sampling pattern and corresponding deep-learning-based reconstruction. METHODS: For k-space down-sampling, a customized pattern was proposed for CEST, with the randomized probability following a frequency-offset-dependent (FOD) function in the direction of saturation offset. For reconstruction, the convolution network (CNN) was enhanced with a Partially Separable (PS) function to optimize the spatial domain and frequency domain separately. Retrospective experiments on a self-acquired human brain dataset (13 healthy adults and 15 brain tumor patients) were conducted using k-space resampling. The prospective performance was also assessed on six healthy subjects. RESULTS: In retrospective experiments, the combination of FOD sampling and PS network (FOD + PSN) showed the best quantitative metrics for reconstruction, outperforming three other combinations of conventional sampling with varying density and a regular CNN (nMSE and SSIM, p < 0.001 for healthy subjects). Across all acceleration factors from 4 to 14, the FOD + PSN approach consistently outperformed the comparative methods in four contrast maps including MTRasym, MTRrex, as well as the Lorentzian Difference maps of amide and nuclear Overhauser effect (NOE). In the subspace replacement experiment, the error distribution demonstrated the denoising benefits achieved in the spatial subspace. Finally, our prospective results obtained from healthy adults and brain tumor patients (14×) exhibited the initial feasibility of our method, albeit with less accurate reconstruction than retrospective ones. CONCLUSION: The combination of FOD sampling and PSN reconstruction enabled highly accelerated CEST MRI acquisition, which may facilitate CEST metabolic MRI for brain tumor patients.

Cas9-Guide RNA Directed Genome Editing in Soybean.

Recently discovered bacteria and archaea adaptive immune system consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) endonuclease has been explored in targeted genome editing in different species. Streptococcus pyogenes Cas9-guide RNA (gRNA) was successfully applied to generate targeted mutagenesis, gene integration, and gene editing in soybean (Glycine max). Two genomic sites, DD20 and DD43 on chromosome 4, were mutagenized with frequencies of 59% and 76%, respectively. Sequencing randomly selected transgenic events confirmed that the genome modifications were specific to the Cas9-gRNA cleavage sites and consisted of small deletions or insertions. Targeted gene integrations through homology-directed recombination were detected by border-specific polymerase chain reaction analysis for both sites at callus stage, and one DD43 homology-directed recombination event was transmitted to T1 generation. T1 progenies of the integration event segregated according to Mendelian laws and clean homozygous T1 plants with the donor gene precisely inserted at the DD43 target site were obtained. The Cas9-gRNA system was also successfully applied to make a directed P178S mutation of acetolactate synthase1 gene through in planta gene editing.

Tissue-specific expression of a soybean hypersensitive-induced response (HIR) protein gene promoter.

A Glycine max gene encoding a putative protein similar to hypersensitive-induced response proteins (HIR) was identified as a gene with preferred expressions in flowers and developing seeds by whole transcriptome gene expression profiling. Its promoter gm-hir1 was cloned and revealed to strongly express a fluorescence reporter gene primarily in integuments, anther tapetum, and seed coat with unique tissue-specificity. Expression in the inner integument was apparent prior to pollination, while expression in the outer integument started to develop from the micropylar end outward as the embryo matured. A 5'-deletion study showed that the promoter can be truncated to 600 bp long relative to the translation start site without affecting expression. A positive regulatory element was identified between 600 and 481 bp that controls expression in the inner integument, with no noticeable effect on expression in the outer integument or tapetum. Additionally, removal of the 5'UTR intron had no effect on levels or location of gm-hir1 expression while truncation to 370 bp resulted in a complete loss of expression suggesting that elements controlling both the outer integument and tapetum expression are located within the 481-370 bp region.

Technical Note: Swing golden angle - A navigator-interleaved golden angle trajectory with eddy current suppression - Application in free-running cardiac MRI.

BACKGROUND: Golden angle (GA) radial trajectory is advantageous for dynamic magnetic resonance imaging (MRI). Recently, several advanced algorithms have been developed based on navigator-interleaved GA trajectory to realize free-running cardiac MRI. However, navigator-interleaved GA trajectory suffers from the eddy-current effect, which reduces the image quality. PURPOSE: This work aims to integrate the navigator-interleaved GA trajectory with clinical cardiac MRI acquisition, with the minimum eddy-current artifacts. The ultimate goal is to realize a high-quality free-running cardiac imaging technique. METHODS: In this paper, we propose a new "swing golden angle" (swingGA) radial profile order. SwingGA samples the k-space by rotating back and forth at the generalized golden ratio interval, with smoothly interleaved navigator readouts. The sampling efficiency and angle increment distributions were investigated by numerical simulations. Static phantom imaging experiments were conducted to evaluate the eddy current effect, compared with cartesian, golden angle radial (GA), and tiny golden angle (tGA) trajectories. Furthermore, 12 heart-healthy subjects (aged 21-25 years) were recruited for free-running cardiac imaging with different sampling trajectories. Dynamic images were reconstructed by a low-rank subspace-constrained algorithm. The image quality was evaluated by signal-to-noise-ratio and spectrum analysis in the heart region, and compared with traditional clinical cardiac MRI images. RESULTS: SwingGA pattern achieves the highest sampling efficiency (mSE > 0.925) and the minimum azimuthal angle increment (mAD < 1.05). SwingGA can effectively suppress eddy currents in static phantom images, with the lowest normalized root mean square error (nRMSE) values among radial trajectories. For the in-vivo cardiac images, swingGA enjoys the highest SNR both in the blood pool and myocardium, and contains the minimum level of high-frequency artifacts. The free-running cardiac images have good consistency with traditional clinical cardiac MRI, and the swingGA sampling pattern achieves the best image quality among all sampling patterns. CONCLUSIONS: The proposed swingGA sampling pattern can effectively improve the sampling efficiency and reduce the eddy currents for the navigator-interleaved GA sequence. SwingGA is a promising sampling pattern for free-running cardiac MRI.

COMET: Cross-space Optimization-based Mutual learning network for super-resolution of CEST-MRI.

Chemical Exchange Saturation Transfer Magn-etic Resonance Imaging (CEST-MRI) is a promising approach for detecting tissue metabolic changes. However, due to the constraints of scan time and contrast-noise-ratio, CEST-MRI always exhibits low spatial resolution, hindering the clinical applications especially for detection of small lesions. Many super-resolution (SR) methods have shown good performance in medical images. However, when applied to CEST-MRI, these methods have two shortcomings that may limit their performance. Firstly, CEST-MRI has an additional frequency dimension, but the information along this dimension is not fully utilized. The second is that these SR methods mainly focus on improving the quality of the CEST-weighted images, while the accuracy of the quantitative maps is the most concerned aspect for CEST-MRI. To address these shortcomings, we propose a Cross-space Optimization-based Mutual learning nETwork (COMET) for SR of CEST-MRI. COMET incorporates novel spatio-frequency extraction modules and a mutual learning module to leverage and combine information from both spatial and frequency spaces, thereby enhancing the SR performance. Furthermore, we propose a novel CEST-based normalization loss to address the normalization-induced distribution problem and preserve the sharpness of quantitative maps, enabling more accurate CEST-MRI quantification. COMET is evaluated on an ischemia rat brain dataset and a human brain dataset. The results demonstrate COMET achieves 8-fold SR, providing accurate quantitative maps. Moreover, COMET outperforms all other state-of-the-art SR methods. Additionally, COMET exhibits its potential in prospective study.

Investigation of the Internal Structure of Hardened 3D-Printed Concrete by X-CT Scanning and Its Influence on the Mechanical Performance.

As we know, 3DPC is printed layer by layer compared with mold-casting conventional concrete. Pore structure and layer-to-layer interface are two main aspects of the internal structure for 3DPC, which decide 3DPC's mechanical performance. The layer-to-layer interface caused by printing is specific to 3DPC. The emphasis of this study lies in the layer-to-layer interfaces of 3DPC. The first aim of this study is to quantify the characteristics of the layer-to-layer interface and therefore characterize different aspects of the interfaces. The second aim of this study is to explore how the internal structure of printed concrete influences the mechanical performance of 3DPC. This research set out to design a series of experimental comparisons between 3DPC and casted concrete with the same compositions. Mechanical tests, i.e., compressive stress, ultrasonic Pulse Velocity test, flexural tension, and tension splitting, as well as the Ultrasonic Pulse Velocity test, were performed to check the mechanical performance of 3DPC. Contrary to what has often been expected, the mechanical test results showed the printed concrete has a quality not worse than casted concrete with the same recipe. Meanwhile, the X-ray computed tomography (X-CT) is used to characterize the internal structure, pore shapes, and interfaces of 3DPC. First, the investigation revealed that the lower total porosity and fewer big voids could be the fundamental causes meaning 3DPC has a better mechanical performance than casted concrete. Second, the statistics based on aspect ratio show that the distribution curves follow similar trends, regardless of the printed or casted concrete. Third, this study quantified the depth of the different interfaces for 3DPC. The results suggest that the porosity in an interface varies in a range. The author's pioneer work has contributed to our present understanding of the interfaces of 3DPC.

Accelerated partial separable model using dimension-reduced optimization technique for ultra-fast cardiac MRI.

Objective.Imaging dynamic objects with high temporal resolution is challenging in magnetic resonance imaging (MRI). The partial separable (PS) model was proposed to improve imaging quality by reducing the degrees of freedom of the inverse problem. However, the PS model still suffers from a long acquisition time and an even longer reconstruction time. The main objective of this study is to accelerate the PS model, shorten the time required for acquisition and reconstruction, and maintain good image quality simultaneously.Approach.We proposed to fully exploit the dimension-reduction property of the PS model, which means implementing the optimization algorithm in subspace. We optimized the data consistency term and used a Tikhonov regularization term based on the Frobenius norm of temporal difference. The proposed dimension-reduced optimization technique was validated in free-running cardiac MRI. We have performed both retrospective experiments on a public dataset and prospective experiments onin vivodata. The proposed method was compared with four competing algorithms based on the PS model and two non-PS model methods.Main results.The proposed method has robust performance against a shortened acquisition time or suboptimal hyper-parameter settings, and achieves superior image quality over all other competing algorithms. The proposed method is 20-fold faster than the widely accepted PS+sparse method, enabling image reconstruction to be finished in just a few seconds.Significance.The accelerated PS model has the potential to save a great deal of time in clinical dynamic MRI examinations and is promising for real-time MRI applications.

Undersampled Multi-Contrast MRI Reconstruction Based on Double-Domain Generative Adversarial Network.

Multi-contrast magnetic resonance imaging can provide comprehensive information for clinical diagnosis. However, multi-contrast imaging suffers from long acquisition time, which makes it inhibitive for daily clinical practice. Subsampling k-space is one of the main methods to speed up scan time. Missing k-space samples will lead to inevitable serious artifacts and noise. Considering the assumption that different contrast modalities share some mutual information, it may be possible to exploit this redundancy to accelerate multi-contrast imaging acquisition. Recently, generative adversarial network shows superior performance in image reconstruction and synthesis. Some studies based on k-space reconstruction also exhibit superior performance over conventional state-of-art method. In this study, we propose a cross-domain two-stage generative adversarial network for multi-contrast images reconstruction based on prior full-sampled contrast and undersampled information. The new approach integrates reconstruction and synthesis, which estimates and completes the missing k-space and then refines in image space. It takes one fully-sampled contrast modality data and highly undersampled data from several other modalities as input, and outputs high quality images for each contrast simultaneously. The network is trained and tested on a public brain dataset from healthy subjects. Quantitative comparisons against baseline clearly indicate that the proposed method can effectively reconstruct undersampled images. Even under high acceleration, the network still can recover texture details and reduce artifacts.

Dataset for centrifuge modelling of laterally monotonic loaded monopiles in saturated dense sand.

The presented dataset was collected in seven centrifuge tests, specifically designed for modelling the lateral response of offshore monopiles in dense sand. Two model piles with outer diameter D = 50 mm were loaded laterally at 100 × g. The embedding depths were 3D, 5D, 7D and 9D, with load eccentricity of 5, 10 and 15. Fibre Bragg gratings (FBGs) were used to measure the tensile and compressive strains of the monopiles. The raw data obtained from different sensors during the tests and the analysed data (e.g. soil reaction, pile deflection) are included in separate editable files, enabling future reuse and development of the experimental results.

A straightforward plant prime editing system enabled highly efficient precise editing of rice Waxy gene.

CRISPR Cas9-mediated genome editing is highly efficient at targeted site-specific gene knock-out through NHEJ (Non-Homology End Joining), but ineffective for specific DNA integration through HDR (Homology Directed Repair) for precise gene editing. Base editors can make limited base substitutions but only within restricted small windows of the protospacer. Prime editing has been applied in plants with various degrees of success. However, several questions such as low and inconsistent editing efficiencies across different target sites need to be addressed. We compared two prime editing approaches PE3 and PE2 at two neighboring target sites within rice Waxy gene to partially address those questions. A straightforward PE2 plant prime editing system retrofitted from a regular CRISPR-Cas9 editing system can deliver highly efficient up to 66.7% precise gene editing. Various forms of precise editing including base substitutions, small deletions and insertions can be accurately achieved. The secondary structure variations of different pegRNAs may be the primary reason for inconsistent editing across different target sites and should be the optimization focus to further improve plant prime editing.

Stacking multiple transgenes at a selected genomic site via repeated recombinase-mediated DNA cassette exchanges.

Recombinase-mediated DNA cassette exchange (RMCE) has been successfully used to insert transgenes at previously characterized genomic sites in plants. Following the same strategy, groups of transgenes can be stacked to the same site through multiple rounds of RMCE. A gene-silencing cassette, designed to simultaneously silence soybean (Glycine max) genes fatty acid ω-6 desaturase 2 (FAD2) and acyl-acyl carrier protein thioesterase 2 (FATB) to improve oleic acid content, was first inserted by RMCE at a precharacterized genomic site in soybean. Selected transgenic events were subsequently retransformed with the second DNA construct containing a Yarrowia lipolytica diacylglycerol acyltransferase gene (DGAT1) to increase oil content by the enhancement of triacylglycerol biosynthesis and three other genes, a Corynebacterium glutamicum dihydrodipicolinate synthetase gene (DHPS), a barley (Hordeum vulgare) high-lysine protein gene (BHL8), and a truncated soybean cysteine synthase gene (CGS), to improve the contents of the essential amino acids lysine and methionine. Molecular characterization confirmed that the second RMCE successfully stacked the four overexpression cassettes to the previously integrated FAD2-FATB gene-silencing cassette. Phenotypic analyses indicated that all the transgenes expressed expected phenotypes.

Revealing frequent alternative polyadenylation and widespread low-level transcription read-through of novel plant transcription terminators.

Plant genetic engineering can create transgenic crops with improved characteristics by introducing trait genes through transformation. Appropriate regulatory elements such as promoters and terminators have to be present in certain configurations for the transgenes to be properly expressed. Five terminators native to soybean genes-encoding a MYB family transcription factor (MYB2), a Kunitz trypsin inhibitor (KTI1), a plasma membrane intrinsic protein (PIP1), a translation elongation factor (EF1A2) and a metallothionein protein (MTH1) were cloned and tested for their ability to enable transgene expression, mRNA polyadenylation and transcription termination. The terminators are as good as a control terminator of the potato proteinase inhibitor II gene (PINII) in conferring proper transgene expression, leading to mRNAs with various polyadenylation sites and terminating mRNA transcripts. RNA transcription read-through was detected in all transgenic plants and was quantified by qRT-PCR to be <1% at positions approximately 1 kb downstream of the 5' ends of different terminators. The detection of read-through RNA transcripts of the corresponding endogenous genes up to approximately 1 kb beyond the polyadenylation sites suggests that limited RNA transcription read-through is a normal phenomenon of gene expression. The study also provided more choices of terminators for plant genetic engineering when constructing DNA constructs containing multiple gene expression cassettes.

Site-specific integration of transgenes in soybean via recombinase-mediated DNA cassette exchange.

A targeting method to insert genes at a previously characterized genetic locus to make plant transformation and transgene expression predictable is highly desirable for plant biotechnology. We report the successful targeting of transgenes to predefined soybean (Glycine max) genome sites using the yeast FLP-FRT recombination system. First, a target DNA containing a pair of incompatible FRT sites flanking a selection gene was introduced in soybean by standard biolistic transformation. Transgenic events containing a single copy of the target were retransformed with a donor DNA, which contained the same pair of FRT sites flanking a different selection gene, and a FLP expression DNA. Precise DNA cassette exchange was achieved between the target and donor DNA via recombinase-mediated cassette exchange, so that the donor DNA was introduced at the locus previously occupied by the target DNA. The introduced donor genes expressed normally and segregated according to Mendelian laws.

Potential Molecular Mechanism and Biomarker Investigation for Spinal Cord Injury Based on Bioinformatics Analysis.

This study aimed to explore the detailed molecular mechanism and biomarkers in spinal cord injury (SCI). Gene expression profiles of GSE125630 were downloaded from the Gene Expression Omnibus (GEO) database, and comprised 14 spinal cord tissues, including contusion SCI group (n = 6, unexercised), complete transection group (n = 4, unexercised), and uninjured control group (n = 4, unexercised). Differentially expressed gene (DEG) and time-series gene investigations, functional enrichment analysis, protein-protein interaction (PPI) network construction, characteristic gene-related disease analysis, and TF-target gene interaction studies were performed. A total of 122 DEGs and 409 DEGs were respectively identified in contusion SCI versus control group and complete transection versus control group, respectively. The PPI network investigated 16 characteristic genes including corticotropin-releasing hormone (CRH), tyrosine hydroxylase (TH), and neurotensin (NTS). These genes were mainly enriched in functions involving response to ethanol, corticosterone, and estradiol. Eventually, a TF-target gene interaction network was constructed with nine TFs [including activating transcription factor 3 (ATF3)] and 10 characteristic genes. The results indicate that regulation of osteoblast differentiation and positive regulation of the BMP signaling pathway may be suppressed in the process of SCI. TH may play a pivotal role in the progression of SCI. In addition, DEGs such as CRH and NTS may be novel targets for SCI therapy.

Uniform Expression and Relatively Small Position Effects Characterize Sister Transformants in Maize and Soybean.

Development of transgenic cell lines or organisms for industrial, agricultural, or medicinal applications involves inserting DNA into the target genome in a way that achieves efficacious transgene expression without a deleterious impact on fitness. The genomic insertion site is widely recognized as an important determinant of success. However, the effect of chromosomal location on transgene expression and fitness has not been systematically investigated in plants. Here we evaluate the importance of transgene insertion site in maize and soybean using both random and site-specific transgene integration. We have compared the relative contribution of genomic location on transgene expression levels with other factors, including cis-regulatory elements, neighboring transgenes, genetic background, and zygosity. As expected, cis-regulatory elements and the presence/absence of nearby transgene neighbors can impact transgene expression. Surprisingly, we determined not only that genomic location had the least impact on transgene expression compared to the other factors that were investigated but that the majority of insertion sites recovered supported transgene expression levels that were statistically not distinguishable. All 68 genomic sites evaluated were capable of supporting high-level transgene expression, which was also consistent across generations. Furthermore, multilocation field evaluation detected no to little decrease in agronomic performance as a result of transgene insertion at the vast majority of sites we evaluated with a single construct in five maize hybrid backgrounds.

A Cre/loxP-mediated self-activating gene excision system to produce marker gene free transgenic soybean plants.

Marker-gene-free transgenic soybean plants were produced by isolating a developmentally regulated embryo-specific gene promoter, app1, from Arabidopsis and developing a self-activating gene excision system using the P1 bacteriophage Cre/loxP recombination system. To accomplish this, the Cre recombinase gene was placed under control of the app1 promoter and, together with a selectable marker gene (hygromycin phosphotransferase), were cloned between two loxP recombination sites. This entire sequence was then placed between a constitutive promoter and a coding region for either beta-glucuronidase (Gus) or glyphosate acetyltransferase (Gat). Gene excision would remove the entire sequence between the two loxP sites and bring the coding region to the constitutive promoter for expression. Using this system marker gene excision occurred in over 30% of the stable transgenic events as indicated by the activation of the gus reporter gene or the gat gene in separate experiments. Transgenic plants with 1 or 2 copies of a functional excision-activated gat transgene and without any marker gene were obtained in T0 or T1 generation. This demonstrates the feasibility of using developmentally controlled promoters to mediate marker excision in soybean.

Arabidopsis ABI5 subfamily members have distinct DNA-binding and transcriptional activities.

A small family of novel basic leucine zipper proteins that includes abscisic acid (ABA)-INSENSITIVE 5 (ABI5) binds to the promoter region of the lea class gene Dc3. The factors, referred to as AtDPBFs (Arabidopsis Dc3 promoter-binding factors), were isolated from an immature seed cDNA library. AtDPBFs bind to the embryo specification and ABA-responsive elements in the Dc3 promoter and are unique in that they can interact with cis-elements that do not contain the ACGT core sequence required for the binding of most other plant basic leucine zipper proteins. Analysis of full-length cDNAs showed that at least five different Dc3 promoter-binding factors are present in Arabidopsis seeds; one of these, AtDPBF-1, is identical to ABI5. As expected, AtDPBF-1/ABI5 mRNA is inducible by exogenous ABA in seedlings. Despite the near identity in their basic domains, AtDPBFs are distinct in their DNA-binding, dimerization, and transcriptional activity.

Stimulation of the cell cycle and maize transformation by disruption of the plant retinoblastoma pathway.

The genome of the Mastreviruses encodes a replication-associated protein (RepA) that interacts with members of the plant retinoblastoma-related protein family, which are putative cell cycle regulators. Expression of ZmRb1, a maize retinoblastoma-related gene, and RepA inhibited and stimulated, respectively, cell division in tobacco cell cultures. The effect of RepA was mitigated by over-expression of ZmRb1. RepA increased transformation frequency and callus growth rate of high type II maize germplasm. RepA-containing transgenic maize calli remained embryogenic, were readily regenerable, and produced fertile plants that transmitted transgene expression in a Mendelian fashion. In high type II, transformation frequency increased with the strength of the promoter driving RepA expression. When a construct in which RepA was expressed behind its native LIR promoter was used, primary transformation frequencies did not improve for two elite Pioneer maize inbreds. However, when LIR:RepA-containing transgenic embryos were used in subsequent rounds of transformation, frequencies were higher in the RepA+ embryos. These data demonstrate that RepA can stimulate cell division and callus growth in culture, and improve maize transformation.