Electrochemical Oxidation Enables Radical Dearomative Spiroannulation to 2H-Spiro[benzofuran-3,9'-fluoren]-2-one.

Developing pragmatic strategies for accessing functional benzofuran-2-ones from 3-([1,1'-biphenyl]-2-yl)benzofuran remains an enduring challenge. Herein, we have achieved a highly discriminating electrochemical oxidative dearomative spiroannulation of 3-([1,1'-biphenyl]-2-yl)benzofuran, culminating in the synthesis of 2H-spiro[benzofuran-3,9'-fluoren]-2-one derivatives. By harnessing the electrophilic intermediates of benzofuryl radical cations supported by DFT calculations, we attain exceptional regioselectivity while eliminating the need for stoichiometric oxidants. Mechanistic investigations reveal a sequence of events involving the benzofuran radical cation, encompassing the capture of H2O, nucleophilic arene attack, and subsequent deprotonation, ultimately yielding the final benzofuran-2-ones.

A Perifacial EMG Acquisition System for Facial-Muscle-Movement Recognition.

This paper proposes a portable wireless transmission system for the multi-channel acquisition of surface electromyography (EMG) signals. Because EMG signals have great application value in psychotherapy and human-computer interaction, this system is designed to acquire reliable, real-time facial-muscle-movement signals. Electrodes placed on the surface of a facial-muscle source can inhibit facial-muscle movement due to weight, size, etc., and we propose to solve this problem by placing the electrodes at the periphery of the face to acquire the signals. The multi-channel approach allows this system to detect muscle activity in 16 regions simultaneously. Wireless transmission (Wi-Fi) technology is employed to increase the flexibility of portable applications. The sampling rate is 1 KHz and the resolution is 24 bit. To verify the reliability and practicality of this system, we carried out a comparison with a commercial device and achieved a correlation coefficient of more than 70% on the comparison metrics. Next, to test the system's utility, we placed 16 electrodes around the face for the recognition of five facial movements. Three classifiers, random forest, support vector machine (SVM) and backpropagation neural network (BPNN), were used for the recognition of the five facial movements, in which random forest proved to be practical by achieving a classification accuracy of 91.79%. It is also demonstrated that electrodes placed around the face can still achieve good recognition of facial movements, making the landing of wearable EMG signal-acquisition devices more feasible.

MolMiner: You Only Look Once for Chemical Structure Recognition.

Molecular structures are commonly depicted in 2D printed forms in scientific documents such as journal papers and patents. However, these 2D depictions are not machine readable. Due to a backlog of decades and an increasing amount of printed literatures, there is a high demand for translating printed depictions into machine-readable formats, which is known as Optical Chemical Structure Recognition (OCSR). Most OCSR systems developed over the last three decades use a rule-based approach, which vectorizes the depiction based on the interpretation of vectors and nodes as bonds and atoms. Here, we present a practical software called MolMiner, which is primarily built using deep neural networks originally developed for semantic segmentation and object detection to recognize atom and bond elements from documents. These recognized elements can be easily connected as a molecular graph with a distance-based construction algorithm. MolMiner gave state-of-the-art performance on four benchmark data sets and a self-collected external data set from scientific papers. As MolMiner performed similarly well in real-world OCSR tasks with a user-friendly interface, it is a useful and valuable tool for daily applications. The free download links of Mac and Windows versions are available at https://github.com/iipharma/pharmamind-molminer.

Transcriptome Analysis of Air Space-Type Variegation Formation in Trifolium pratense.

Air space-type variegation is the most diverse among the species of known variegated leaf plants and is caused by conspicuous intercellular spaces between the epidermal and palisade cells and among the palisade cells at non-green areas. Trifolium pratense, a species in Fabaceae with V-shaped air space-type variegation, was selected to explore the application potential of variegated leaf plants and accumulate basic data on the molecular regulatory mechanism and evolutionary history of leaf variegation. We performed comparative transcriptome analysis on young and adult leaflets of variegated and green plants and identified 43 candidate genes related to air space-type variegation formation. Most of the genes were related to cell-wall structure modification (CESA, CSL, EXP, FLA, PG, PGIP, PLL, PME, RGP, SKS, and XTH family genes), followed by photosynthesis (LHCB subfamily, RBCS, GOX, and AGT family genes), redox (2OG and GSH family genes), and nitrogen metabolism (NodGS family genes). Other genes were related to photooxidation, protein interaction, and protease degradation systems. The downregulated expression of light-responsive LHCB subfamily genes and the upregulated expression of the genes involved in cell-wall structure modification were important conditions for air space-type variegation formation in T. pratense. The upregulated expression of the ubiquitin-protein ligase enzyme (E3)-related genes in the protease degradation systems were conducive to air space-type variegation formation. Because these family genes are necessary for plant growth and development, the mechanism of the leaf variegation formation in T. pratense might be a widely existing regulation in air space-type variegation in nature.

Lightweight and Efficient Image Dehazing Network Guided by Transmission Estimation from Real-World Hazy Scenes.

In this paper, a transmission-guided lightweight neural network called TGL-Net is proposed for efficient image dehazing. Unlike most current dehazing methods that produce simulated transmission maps from depth data and haze-free images, in the proposed work, guided transmission maps are computed automatically using a filter-refined dark-channel-prior (F-DCP) method from real-world hazy images as a regularizer, which facilitates network training not only on synthetic data, but also on natural images. A double-error loss function that combines the errors of a transmission map with the errors of a dehazed image is used to guide network training. The method provides a feasible solution for introducing priors obtained from traditional non-learning-based image processing techniques as a guide for training deep neural networks. Extensive experimental results demonstrate that, in terms of several reference and non-reference evaluation criteria for real-world images, the proposed method can achieve state-of-the-art performance with a much smaller network size and with significant improvements in efficiency resulting from the training guidance.

Hybridization, polyploidization, and morphological convergence make dozens of taxa into one chaotic genetic pool: a phylogenomic case of the Ficus erecta species complex (Moraceae).

The Ficus erecta complex, characterized by its morphological diversity and frequent interspecific overlap, shares pollinating fig wasps among several species. This attribute, coupled with its intricate phylogenetic relationships, establishes it as an exemplary model for studying speciation and evolutionary patterns. Extensive researches involving RADseq (Restriction-site associated DNA sequencing), complete chloroplast genome data, and flow cytometry methods were conducted, focusing on phylogenomic analysis, genetic structure, and ploidy detection within the complex. Significantly, the findings exposed a pronounced nuclear-cytoplasmic conflict. This evidence, together with genetic structure analysis, confirmed that hybridization within the complex is a frequent occurrence. The ploidy detection revealed widespread polyploidy, with certain species exhibiting multiple ploidy levels, including 2×, 3×, and 4×. Of particular note, only five species (F. abelii, F. erecta, F. formosana, F. tannoensis and F. vaccinioides) in the complex were proved to be monophyletic. Species such as F. gasparriniana, F. pandurata, and F. stenophylla were found to encompass multiple phylogenetically distinct lineages. This discovery, along with morphological comparisons, suggests a significant underestimation of species diversity within the complex. This study also identified F. tannoensis as an allopolyploid species originating from F. vaccinioide and F. erecta. Considering the integration of morphological, molecular systematics, and cytological evidences, it is proposed that the scope of the F. erecta complex should be expanded to the entire subsect. Frutescentiae. This would redefine the complex as a continuously evolving group comprising at least 33 taxa, characterized by blurred species boundaries, frequent hybridization and polyploidization, and ambiguous genetic differentiation.

Plant Defense and Viral Counter-Defense during Plant-Geminivirus Interactions.

Geminiviruses are the largest family of plant viruses that cause severe diseases and devastating yield losses of economically important crops worldwide. In response to geminivirus infection, plants have evolved ingenious defense mechanisms to diminish or eliminate invading viral pathogens. However, increasing evidence shows that geminiviruses can interfere with plant defense response and create a suitable cell environment by hijacking host plant machinery to achieve successful infections. In this review, we discuss recent findings about plant defense and viral counter-defense during plant-geminivirus interactions.

Source-oriented ecological and resistome risks associated with geochemical enrichment of heavy metals in river sediments.

Heavy metals (HMs) pose ecological and resistome risks to aquatic systems. To efficiently develop targeted risk mitigation strategies, apportioning HM sources and assessing their source-oriented risks are essential. Although many studies have reported risk assessment and source apportionment of HMs, yet few have explored source-specific ecological and resistome risks associated with geochemical enrichment of HMs in aquatic environments. Therefore, this study proposes an integrated technological framework to characterize source-oriented ecological and resistome risks in the sediments of a plain river in China. Several geochemical tools quantitatively showed Cd and Hg had the highest pollution levels in the environment, with 19.7 and 7.5 times higher than their background values, respectively. Positive matrix factorization (PMF) and Unmix were comparatively used to apportion sources of HMs. Essentially, the two models were complementary and identified similar sources including industrial discharges, agricultural activities, atmospheric deposition and natural background, with contributions of 32.3-37.0%, 8.0-9.0%, 12.1-15.9% and 42.8-43.0%, respectively. To analyze source-specific ecological risks, the apportionment results were integratively incorporated into a modified ecological risk index. The results showed anthropogenic sources were the most significant contributors to the ecological risks. Particularly, industrial discharges majorly contributed high- (44%) and extremely high (52%) ecological risk for Cd, while agricultural activities posed a greater percentage of considerable-(36%) and high- (46%) ecological risk for Hg. Furthermore, the high-throughput sequencing metagenomic analysis identified abundant and diverse antibiotic resistance genes (ARGs), including some carbapenem-resistance genes and emerging genes such as mcr-type in the river sediments. Network and statistical analyses displayed significant correlations between ARGs and geochemical enrichment of HMs (ρ > 0.8; P-value <0.01), indicating their important impacts on resistome risks in the environment. This study provides useful insights into risk prevention and pollution control of HMs, and the framework can be made applicable to other rivers facing environmental challenges worldwide.

Ficusmotuoensis (Moraceae), a new species from southwest China.

A new climbing species, Ficusmotuoensis Zhen Zhang & Hong Qing Li in Moraceae from southwest China has been described and illustrated in this paper. The new species resembles F.disticha, F.diversiformis and F.hederacea, but differs from these in the medium-sized acrophylls, shorter peduncle, as well as larger and spotted syconium. According to the morphological traits and phylogenetic placement, the new species belongs to Ficussubg.Synoeciasect.Apiosycea. Besides, the new species deviates from the common distribution pattern compared to the other members of sect. Apiosycea, indicating that it could be very useful for exploring the biogeography of sect. Apiosycea.

Development of chloroplast genome resources for peanut (Arachis hypogaea L.) and other species of Arachis.

ABSRACT: Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. Wild Arachis spp. are potental sources of novel genes for the genetic improvement of cultivated peanut. Understanding the genetic relationships with cultivated peanut is important for the efficient use of wild species in breeding programmes. However, for this genus, only a few genetic resources have been explored so far. In this study, new chloroplast genomic resources have been developed for the genus Arachis based on whole chloroplast genomes from seven species that were sequenced using next-generation sequencing technologies. The chloroplast genomes ranged in length from 156,275 to 156,395 bp, and their gene contents, gene orders, and GC contents were similar to those for other Fabaceae species. Comparative analyses among the seven chloroplast genomes revealed 643 variable sites that included 212 singletons and 431 parsimony-informative sites. We also identified 101 SSR loci and 85 indel mutation events. Thirty-seven SSR loci were found to be polymorphic by in silico comparative analyses. Eleven highly divergent DNA regions, suitable for phylogenetic and species identification, were detected in the seven chloroplast genomes. A molecular phylogeny based on the complete chloroplast genome sequences provided the best resolution of the seven Arachis species.

Genome-Wide Association Study of Major Agronomic Traits Related to Domestication in Peanut.

Peanut (Arachis hypogaea) consists of two subspecies, hypogaea and fastigiata, and has been cultivated worldwide for hundreds of years. Here, 158 peanut accessions were selected to dissect the molecular footprint of agronomic traits related to domestication using specific-locus amplified fragment sequencing (SLAF-seq method). Then, a total of 17,338 high-quality single nucleotide polymorphisms (SNPs) in the whole peanut genome were revealed. Eleven agronomic traits in 158 peanut accessions were subsequently analyzed using genome-wide association studies (GWAS). Candidate genes responsible for corresponding traits were then analyzed in genomic regions surrounding the peak SNPs, and 1,429 genes were found within 200 kb windows centerd on GWAS-identified peak SNPs related to domestication. Highly differentiated genomic regions were observed between hypogaea and fastigiata accessions using FST values and sequence diversity (π) ratios. Among the 1,429 genes, 662 were located on chromosome A3, suggesting the presence of major selective sweeps caused by artificial selection during long domestication. These findings provide a promising insight into the complicated genetic architecture of domestication-related traits in peanut, and reveal whole-genome SNP markers of beneficial candidate genes for marker-assisted selection (MAS) in future breeding programs.

Microsatellites for Phytolacca acinosa (Phytolaccaceae), a traditional medicinal herb.

PREMISE OF THE STUDY: Phytolacca acinosa (Phytolaccaceae) is a traditional Chinese herb with multiple medicinal uses and is an important pigment source. Due to excessive human harvesting, the population numbers and sizes have decreased dramatically. METHODS AND RESULTS: Using an enriched genomic library, we developed and characterized 15 microsatellite primers for P. acinosa, 13 of which were polymorphic. The number of alleles varied from two to seven. The observed heterozygosity and expected heterozygosity per locus ranged from 0.267 to 1.000 and 0.331 to 0.743, respectively. All of the primers that were developed were also successfully applied in P. americana. CONCLUSIONS: These markers should be useful in probing the genetic diversity, genetic structure, and mating systems of P. acinosa, which could provide information about protecting and sustainably harvesting this species.

Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size.

Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01). These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11-15.