Antifungal mechanism of cell-free supernatant produced by Trichoderma virens and its efficacy for the control of pear Valsa canker.

Introduction: Pear Valsa canker, caused by Valsa pyri (V. pyri), poses a major threat to pear production. We aimed to assess the effectiveness of the cell-free supernatant (CFS) produced by Trichoderma virens (T. virens) to control the development of pear Valsa canker and reveal the inhibitory mechanism against the pathogenic fungi. Results: Using morphological characteristics and phylogenetic analysis, the pathogen G1H was identified as V. pyri, and the biocontrol fungus WJ561 was identified as Trichoderma virens. CFS derived from WJ561 exhibited strong inhibition of mycelial growth and was capable of reducing the pathogenicity of V. pyri on pear leaves and twigs. Scanning electron microscopy (SEM) observations revealed deformations and shrinkages in the fungal hyphae treated with CFS. The CFS also destroyed the hyphal membranes leading to the leakage of cellular contents and an increase in the malondialdehyde (MDA) content. Additionally, CFS significantly inhibited the activities of catalase (CAT) and superoxide dismutase (SOD), and downregulated the expression of antioxidant defense-related genes in V. pyri, causing the accumulation of reactive oxygen species (ROS). Artesunate, identified as the main component in CFS by liquid chromatograph-mass spectrometry (LC-MS), exhibited antifungal activity against V. pyri. Conclusion: Our findings demonstrate the promising potential of T. virens and its CFS in controlling pear Valsa canker. The primary inhibitory mechanism of CFS involves multiple processes, including membrane damage and negatively affecting enzymatic detoxification pathways, consequently leading to hyphal oxidative damage of V. pyri. This study lays a theoretical foundation for the utilization of T. virens to control V. pyri in practical production.

Improving accelerated MRI by deep learning with sparsified complex data.

PURPOSE: To obtain high-quality accelerated MR images with complex-valued reconstruction from undersampled k-space data. METHODS: The MRI scans from human subjects were retrospectively undersampled with a regular pattern using skipped phase encoding, leading to ghosts in zero-filling reconstruction. A complex difference transform along the phase-encoding direction was applied in image domain to yield sparsified complex-valued edge maps. These sparse edge maps were used to train a complex-valued U-type convolutional neural network (SCU-Net) for deghosting. A k-space inverse filtering was performed on the predicted deghosted complex edge maps from SCU-Net to obtain final complex images. The SCU-Net was compared with other algorithms including zero-filling, GRAPPA, RAKI, finite difference complex U-type convolutional neural network (FDCU-Net), and CU-Net, both qualitatively and quantitatively, using such metrics as structural similarity index, peak SNR, and normalized mean square error. RESULTS: The SCU-Net was found to be effective in deghosting aliased edge maps even at high acceleration factors. High-quality complex images were obtained by performing an inverse filtering on deghosted edge maps. The SCU-Net compared favorably with other algorithms. CONCLUSION: Using sparsified complex data, SCU-Net offers higher reconstruction quality for regularly undersampled k-space data. The proposed method is especially useful for phase-sensitive MRI applications.

Benzalkonium Chloride and Benzethonium Chloride Effectively Reduce Spore Germination of Ginger Soft Rot Pathogens: Fusarium solani and Fusarium oxysporum.

Ginger soft rot is a serious soil-borne disease caused by Fusarium solani and Fusarium oxysporum, resulting in reduced crop yields. The application of common chemical fungicides is considered to be an effective method of sterilization, and therefore, they pose a serious threat to the environment and human health due to their high toxicity. Benzalkonium chloride (BAC) and benzethonium chloride (BEC) are two popular quaternary ammonium salts with a wide range of fungicidal effects. In this study, we investigated the fungicidal effects of BAC and BEC on soft rot disease of ginger as alternatives to common chemical fungicides. Two soft rot pathogens of ginger were successfully isolated from diseased ginger by using the spread plate method and sequenced as F. solani and F. oxysporum using the high-throughput fungal sequencing method. We investigated the fungicidal effects of BAC and BEC on F. solani and F. oxysporum, and we explored the antifungal mechanisms. Almost complete inactivation of spores of F. solani and F. oxysporum was observed at 100 mg/L fungicide concentration. Only a small amount of spore regrowth was observed after the inactivation treatment of spores of F. solani and F. oxysporum in soil, which proved that BAC and BEC have the potential to be used as an alternative to common chemical fungicides for soil disinfection of diseased ginger.

Replicative bypass studies of l-deoxyribonucleosides in Vitro and in E. coli cell.

L-nucleosides were the most important antiviral lead compounds because they can inhibit viral DNA polymerase and DNA synthesis of many viruses, whereas they may lead to mutations in DNA replication and cause genomic instability. In this study, we reported the replicative bypass of L-deoxynucleosides in recombinant DNA by restriction enzyme-mediated assays to examine their impact on DNA replication in vitro and in E. coli cells. The results showed that a template L-dC inhibited Taq DNA polymerase reaction, whereas it can be bypassed by Vent (exo-) DNA polymerase as well as in cell replication, inserting correct nucleotides opposite L-dC. L-dG can be bypassed by Taq DNA polymerase and in E. coli cells, maintaining insertion of correct incoming nucleotides, and L-dG induced mutagenic replication by Vent (exo-) DNA polymerase. In contrast, L-dA can induced mutagenic replication in vitro and in E. coli cells. MD simulations were performed to investigate how DNA polymerase affected replicative bypass and mutations when D-nucleosides replaced with L-nucleosides. This study will provide a basis for the ability to assess the cytotoxic and mutagenic properties of the L-nucleoside drugs.

Highly Stretchable, Fatigue-Resistant, Electrically Conductive, and Temperature-Tolerant Ionogels for High-Performance Flexible Sensors.

Ionogels are ideal candidate materials for flexible sensors, but their stretchability and fatigue resistance are limited. Herein, highly stretchable, fatigue-resistant, electrically conductive, and temperature-tolerant ionogels are investigated and further applied in fabricating high-performance flexible sensors. The ionogels consist of a poly(acrylic acid) (PAA) network and a commonly used room-temperature ionic liquid (RTIL) named 1-ethyl-3-methylimidazolium dicyanamide ([EMIm][DCA]). Dually acrylated Pluronic F127 (F127DA) was utilized to cross-link the PAA network, and [EMIm][DCA] was physically confined in the PAA network. Because of their special cross-linking structure, the PAA ionogels are highly stretchable (>850%), tough, and fatigue-resistant, and they are also conductive, transparent, and temperature-tolerant because of the existence of [EMIm][DCA]. On the basis of their integrated performances, the PAA ionogels were further utilized to fabricate strain sensors and pressure sensors. The ionogel-based strain sensors have high sensitivity, low response time (200 ms), wide strain-sensing range (0-750%), excellent durability (>1400 cycles), and good temperature tolerance and can be applied to detect various human motions. The pressure sensors also have a high response speed (256 ms) and excellent sensitivity (GF = 0.73 kPa-1), which offers an opportunity to detect force generated by finger touching and water droplets.

Improving image quality for skipped phase encoding and edge deghosting (SPEED) by exploiting several sparsifying transforms.

PURPOSE: To improve the image quality of skipped phase encoding and edge deghosting (SPEED) by exploiting several sparsifying transforms. METHODS: The SPEED technique uses a skipped phase encoding (PE) step to accelerate MRI scan. Previously, a difference transform (DT) along PE direction is used to obtain sparse ghosted-edge maps, which were modeled by a double layer ghost model and was then deghosted by a least square error solution. In this work, it is hypothesized that enhanced sparsity, and thus improved image quality may be achievable with other sparsifying transforms, including discrete wavelet transform (DWT), discrete cosine transform (DCT), DWT combined with DT, and DCT combined with DT. RESULTS: For images of human subjects, SPEED with DWT or DCT can yield higher image quality than DT only, especially for those images with low contrast. Reconstruction error can be further reduced if DWT or DCT are combined with DT. CONCLUSION: Image sparsity can be enhanced with more advanced transforms, leading to higher reconstruction quality in SPEED imaging that is desirable for practical MRI applications.

Aliasing Artefact Suppression in Compressed Sensing MRI for Random Phase-Encode Undersampling.

GOAL: Random phase-encode undersampling of Cartesian k-space trajectories is widely implemented in compressed sensing (CS) MRI. However, its one-dimensional (1-D) randomness inherently introduces large coherent aliasing artefacts along the undersampled direction in the reconstruction and, thus, degrades the image quality. This paper proposes a novel reconstruction scheme to reduce the 1-D undersampling-induced aliasing artefacts. METHODS: The proposed reconstruction progress is separated into two steps in our new algorithm. In step one, we transfer the original two-dimensional (2-D) image reconstruction into a parallel 1-D signal reconstruction procedure, which takes advantage of the superior incoherence property in the phase direction. In step two, using the new k-space data obtained from the 1-D reconstructions, we implement a follow-up 2-D CS reconstruction to produce a better solution, which exploits the inherent correlations between the adjacent lines of 1-D reconstructed signals. RESULTS: We evaluated the performance on various cases of typical MR images, including cardiac cine, brain, foot, and angiogram at the reduction factor up to 10 and compared the results with the conventional CS method. Experiments using the proposed method demonstrated faithful reconstruction of the MR images. CONCLUSION: Compared with conventional method, the new method achieves more accurate reconstruction results with 2-5 dB gain in peak SNR and higher structural similarity index. SIGNIFICANCE: The proposed method improves image quality of the reconstructions and suppresses the coherent artefacts introduced by the random phase-encode undersampling.

Background-suppressed MR venography of the brain using magnitude data: a high-pass filtering approach.

Conventional susceptibility-weighted imaging (SWI) uses both phase and magnitude data for the enhancement of venous vasculature and, thus, is subject to signal loss in regions with severe field inhomogeneity and in the peripheral regions of the brain in the minimum-intensity projection. The purpose of this study is to enhance the visibility of the venous vasculature and reduce the artifacts in the venography by suppressing the background signal in postprocessing. A high-pass filter with an inverted Hamming window or an inverted Fermi window was applied to the Fourier domain of the magnitude images to enhance the visibility of the venous vasculature in the brain after data acquisition. The high-pass filtering approach has the advantages of enhancing the visibility of small veins, diminishing the off-resonance artifact, reducing signal loss in the peripheral regions of the brain in projection, and nearly completely suppressing the background signal. The proposed postprocessing technique is effective for the visualization of small venous vasculature using the magnitude data alone.

Accelerated MRI by SPEED with generalized sampling schemes.

PURPOSE: To enhance the fast imaging technique of skipped phase encoding (PE) and edge deghosting (SPEED) for more general sampling options, and thus more flexibility in implementations and applications. METHODS: SPEED uses skipped PE steps to accelerate MRI scan. Previously, the PE skip size was chosen from prime numbers only. This restriction has been relaxed in this study to allow choice of any integers rather than merely prime numbers. Various sampling patterns were studied under all possible combinations of PE skip size and PE shifts. A criterion based on the rank values of ghost phasor matrices was introduced to evaluate SPEED reconstruction. RESULTS: The reconstruction quality was found to correlate with the rank value of the ghost phasor matrix and the skipped PE size N. A low-rank value indicates a singular matrix that causes failure of the SPEED reconstruction. Composite numbers combined with appropriately chosen PE shifts yielded satisfactory reconstruction results. CONCLUSION: With properly chosen PE shifts, it was found that any integers, including both prime numbers and composite numbers, could be used as PE skip size for SPEED. This finding allows much more flexible data acquisition options that may lead to more freedom in practical implementations and applications.

MR venography of the brain with enhanced vessel contrast using image-domain high-pass filtering of the susceptibility phase shift.

PURPOSE: To develop a postprocessing algorithm that enhances the visibility of intracranial venous vasculature and reduces the artifacts in the display of susceptibility-weighted images (SWI). MATERIALS AND METHODS: Image-domain high-pass filters based on second-order phase difference were applied to the complex 3D SWI data to enhance the susceptibility phase shift of the veins and suppress background signal in SWI. A multivariant statistical parameter was used to suppress the noise in air. RESULTS: Magnetic resonance (MR) venography with enhanced susceptibility phase shift and reduced off-resonance artifacts was obtained using the proposed filters. The background signal in the 3D MR venography data was well suppressed. Venous vasculature in the peripheral regions of the brain was well depicted and the adverse effect of noise in air in the maximum-intensity projection display of the 3D SWI data was well suppressed. CONCLUSION: Image-domain high-pass filtering with second-order phase difference provides an alternative display of 3D SWI data with enhanced visibility of the venous vasculature and effective suppression of artifacts.

Robust tissue-air volume segmentation of MR images based on the statistics of phase and magnitude: Its applications in the display of susceptibility-weighted imaging of the brain.

PURPOSE: To develop a robust algorithm for tissue-air segmentation in magnetic resonance imaging (MRI) using the statistics of phase and magnitude of the images. MATERIALS AND METHODS: A multivariate measure based on the statistics of phase and magnitude was constructed for tissue-air volume segmentation. The standard deviation of first-order phase difference and the standard deviation of magnitude were calculated in a 3 x 3 x 3 kernel in the image domain. To improve differentiation accuracy, the uniformity of phase distribution in the kernel was also calculated and linear background phase introduced by field inhomogeneity was corrected. The effectiveness of the proposed volume segmentation technique was compared to a conventional approach that uses the magnitude data alone. RESULTS: The proposed algorithm was shown to be more effective and robust in volume segmentation in both synthetic phantom and susceptibility-weighted images of human brain. Using our proposed volume segmentation method, veins in the peripheral regions of the brain were well depicted in the minimum-intensity projection of the susceptibility-weighted images. CONCLUSION: Using the additional statistics of phase, tissue-air volume segmentation can be substantially improved compared to that using the statistics of magnitude data alone.

Multi-echo acquisition of MR angiography and venography of the brain at 3 Tesla.

PURPOSE: To improve the visibility of veins in susceptibility-weighted imaging (SWI) using a multi-gradient echo acquisition. MATERIALS AND METHODS: A three-dimensional multi-echo gradient-echo pulse sequence was developed for simultaneous acquisition of MR angiography and multiple volumes of MR venography (MRV) of the brain. The first echo was acquired for MR angiography using the time-of-flight in-flow effect. The subsequent echoes were acquired for SWI-based MRV at different echo times (TEs). RESULTS: Multiple MRV datasets acquired at different TEs were complementary in depicting the venous vasculature. MRV data acquired at a longer TE had a higher venous contrast and stronger susceptibility weighting, whereas MRV data acquired at a shorter TE had a higher signal-to-noise ratio and less severe off-resonance artifacts. Three-dimensional mapping of local field gradients was calculated and the transverse relaxivity (R(2)) at each voxel was quantified using multi-TE exponential fitting. CONCLUSION: Multi-echo acquisition of MR angiography and venography demonstrated improved visibility of venous vasculature especially in regions with severe field inhomogeneity compared with conventional acquisition of SWI and dual-echo acquisition of MR angiography and venography.

Reduction of artifacts in susceptibility-weighted MR venography of the brain.

PURPOSE: To reduce the off-resonance artifact in susceptibility-weighted imaging (SWI)-based MR venography (MRV) in the brain regions with severe field inhomogeneity and to reduce the signal loss in the minimum-intensity projection (mIP) display of the 3D MRV. MATERIALS AND METHODS: A novel postprocessing approach was presented to map the local field gradients (LFGs) using the 3D SWI data without phase-unwrapping. LFG measurements were used to assess the severity of field inhomogeneity and suppress the residual phase in the phase mask induced by the off-resonance effect. Volume segmentation of brain tissue was used to reduce the signal loss in the peripheral regions of the brain in the through-plane mIP images and enable in-plane mIP display of MRV. RESULTS: Off-resonance artifact in the brain regions with severe field inhomogeneity was effectively reduced by the LFG-based phase suppression approach. Signal loss was reduced in the through-plane mIP of MRV using volume segmentation of brain tissue prior to projection. In-plane mIP of MRV also became feasible with volume segmentation. CONCLUSION: Off-resonance artifacts and signal loss in mIP display of MRV can be effectively reduced through postprocessing.

Simultaneous acquisition of MR angiography and venography (MRAV).

A dual-echo pulse sequence for simultaneous acquisition of MR angiography and venography (MRAV) is developed. Data acquisition of the second echo for susceptibility-weighted imaging-based MR venography is added to the conventional three-dimensional (3D) time-of-flight (TOF) MRA pulse sequence. Using this dual-echo acquisition approach, the venography data can be acquired without increasing the repetition time, and, therefore, the scan duration of routine TOF MRA scans is maintained. The feasibility of simultaneous acquisition of MRAV is presented in brain scans at different spatial resolutions. The effect of spatial resolution on vein-to-background contrast is also demonstrated. Venous contrast is improved in high-resolution (0.52 x 0.52 x 1.6 mm(3)) images compared to that in standard-resolution (0.78 x 0.78 x 1.6 mm(3)) images. This MRAV technique enables the acquisition of MR venography without the need of an extra scan or injection of contrast agent in routine clinical brain exams at 3T.

Functional characterization of Drosophila Translin and Trax.

The vertebrate RNA and ssDNA-binding protein Translin has been suggested to function in a variety of cellular processes, including DNA damage response, RNA transport, and translational control. The Translin-associated factor X (Trax) interacts with Translin, and Trax protein stability depends on the presence of Translin. To determine the function of the Drosophila Translin and Trax, we generated a translin null mutant and isolated a trax nonsense mutation. translin and trax single and double mutants are viable, fertile, and phenotypically normal. Meiotic recombination rates and chromosome segregation are also not affected in translin and trax mutants. In addition, we found no evidence for an increased sensitivity for DNA double-strand damage in embryos and developing larvae. Together with the lack of evidence for their involvement in DNA double-strand break checkpoints, this argues against a critical role for Translin and Trax in sensing or repairing such DNA damage. However, Drosophila translin is essential for stabilizing the Translin interaction partner Trax, a function that is surprisingly conserved throughout evolution. Conversely, trax is not essential for Translin stability as trax mutants exhibit normal levels of Translin protein.