Learning based compressive snapshot spectral light field imaging with RGB sensors.

The application of multidimensional optical sensing technologies, such as the spectral light field (SLF) imager, has become increasingly common in recent years. The SLF sensors provide information in the form of one-dimensional spectral data, two-dimensional spatial data, and two-dimensional angular measurements. Spatial-spectral and angular data are essential in a variety of fields, from computer vision to microscopy. Beam-splitters or expensive camera arrays are required for the usage of SLF sensors. The paper describes a low-cost RGB light field camera-based compressed snapshot SLF imaging method. Inspired by the compressive sensing paradigm, the four dimensional SLF can be reconstructed from a measurement of an RGB light field camera via a network which is proposed by utilizing a U-shaped neural network with multi-head self-attention and unparameterized Fourier transform modules. This method is capable of gathering images with a spectral resolution of 10 nm, angular resolution of 9 × 9, and spatial resolution of 622 × 432 within the spectral range of 400 to 700 nm. It provides us an alternative approach to implement the low cost SLF imaging.

Identification and genetic analysis of alternative splicing of long non-coding RNAs in tomato initial flowering stage.

Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play essential regulatory roles in various developmental processes and stress responses. However, the functions of AS lncRNAs during the initial flowering of tomato are largely unknown. This study was designed to investigate the AS pattern of lncRNAs in tomato flower, leaf, and root tissues at the initial flowering stage. Using RNA-Seq, we found that 72.55% of lncRNAs underwent AS in these tissues, yielding a total of 16,995 AS events. Among them, the main type of AS event is alternative first exon (AFE), followed by retained intron (RI). We performed candidate target genes analysis on tissue-specific AS lncRNA, and the results indicated that the candidate target genes of these lncRNAs may be involved in the regulation of circadian rhythm, plant immunity, cellulose synthesis and phosphate-containing compound metabolic process. Moreover, a total of 73,085 putative SNPs and 15,679 InDels were detected, and the potential relationship between the AS of lncRNAs and interesting SNP and InDel loci, as well as their numbers, revealed their effects on tomato genetic diversity and genomic stability. Our data provide new insights into the complexity of the transcriptome and the regulation of AS.

Channeled compressive imaging spectropolarimeter.

A compressive imaging spectropolarimeter is proposed in this paper, capable of simultaneously acquiring full polarization, spatial and spectral information of the object scene. The spectral and polarization information is modulated through a combination of high-order retarders, a dispersion prism and a polarizer filter wheel. Using a random coded aperture, compressive sensing is applied to eliminate the channel crosstalk and resolution limitation of traditional channeled spectropolarimeters. The forward sensing model and inverse problem are developed. Computer simulation results are reported, followed by experimental demonstrations.

Wavelet transform based defringing in interference imaging spectrometer.

The constructive and destructive fringe-like pattern (FP) introduced by the fringing effects is a universal phenomenon emerging in the imaging system using the back-illuminated CCD. Generally, the flat fielding or modeling based methods were applied to suppressing the FP and featured as time-consuming, duplicated, and hardware-based. In this paper, a method based on the wavelet transform was proposed for the interferogram processing in interference imaging spectrometer. An artificial interferogram construction method was developed and utilized to evaluate the quality of the reconstructed interferogram. The performance of defringing was significantly determined by the wavelet decomposition. Through numerical simulation, 4 wavelets were selected out of 50 typical wavelets; the decomposition levels with better performance were determined. The feasibility of the defringing and performance evaluation methods were verified by the simulation and practical experiments. It provides us with a software-based, time-saving, without prior knowledge, automatic approach for defringing.

Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce (Lactuca sativa).

Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase chain reaction (PCR) to validate the candidate circRNA molecules. We then combined bioinformatics approach to explore the function of the parental genes of circRNA, including network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We identified 1650 circRNAs in lettuce, of which 1508 (86.40%) were derived from exons. Using real-time PCR, we characterized 10 validated differentially expressed circRNAs and their parental genes, all of which showed expression patterns consistent with RNA-Seq data. Interestingly, the expression of circRNA was, in some cases, inversely correlated with the expression of the parental gene. Furthermore, analysis of the circRNA-microRNA-mRNA network suggests that circRNAs may be involved in plant hormone signaling and chlorophyll metabolism during photoreactivity. These findings provide an essential reference basis for studying circRNAs' biological mechanisms in light-treated plants.

Impacts of biochar application rates and particle sizes on runoff and soil loss in small cultivated loess plots under simulated rainfall.

Increasing literature suggests that biochar can be used to improve soil fertility and subsequently benefit crop yield. However, the effects of biochar application rates and particle sizes on soil erosion processes have yet to be fully identified. The objective of the present study was to evaluate the influence of biochar with different application rates and particle sizes on soil erosion. Addition of biochar to loess generally increased the mean time to runoff by 19.47% relative to the control. The time to runoff decreased with an increase in the biochar application rates and fluctuated with a decrease in biochar particle sizes. The combined 1% and <0.25 mm biochar treatment yielded the longest time to runoff (2.97 min) and the lowest runoff (36.23 kg m-2 h-1) and soil loss (1.33 kg m-2 min-1). Biochar addition decreased the total runoff volume by 12.21% and generally inhibited soil loss under lower application rates (1% and 3%) while promoting soil loss under higher application rates (5% and 7%). With a decrease in biochar particle size, total runoff volume increased under the 5% and 7% biochar, but no uniform trend was observed under the 1% and 3% biochar treatments. The total soil loss increased with increasing biochar application rates, whereas a negative trend was observed with decreasing biochar particle sizes. The contribution of biochar application rates to runoff and soil loss rates was distinctly greater than the biochar particle sizes. Additionally, biochar addition could increase >2 mm water-stable soil aggregates and saturated hydraulic conductivity (Ksat) in this study. We inferred that the positive effects on soil and water loss were potentially due to the improvement in >2 mm water-stable soil aggregates and Ksat. The results implied that soil-biochar additions could be a potential measure for conserving soil and water in the Loess Plateau.

The infection and impact of Azorhizobium caulinodans ORS571 on wheat (Triticum aestivum L.).

Based on our previous study, cereal crop wheat (Triticum aestivum L.) could be infected by rhizobia Azorhizobium caulinodans ORS571, and form para-nodules with the induction of 2.4-dichlorophenoxyacetic acid, a common plant growth regulator. To enhance this infection and the potential agricultural application, we compared six different infection methods (Direct seed dip; Seed germination dip; Pruned-root dip; Foliar spray; Circum-soil dip; Seed dip and circum-soil dip) for achieving the high efficient infection of A. caulinodans into wheat plants by employing a green fluorescent protein (gfp)-labeled Azorhizobium caulinodans strain ORS571. With proper methods, copious rhizobia could enter the interior and promote the growth of wheat to the hilt. Circum-soil dip was proved to be the most efficient method, seed germination dip and pruned-root dip is the last recommended to infect wheat, seed germination dip and seed dip and circum-soil dip showed better effects on plant growth, pruned-root dip did not show too much effect on plant growth. This study laid the foundation for understanding the interaction between rhizobia and cereal crops and the growth-promoting function of rhizobia.