BackgroundOver 200 published studies of more than 30 plant species have reported a role for miRNAs in regulating responses to abiotic stresses. However, data from these individual reports has not been collected into a single database. The lack of a curated database of stress-related miRNAs limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application.DescriptionPASmiR, a literature-curated and web-accessible database, was developed to provide detailed, searchable descriptions of miRNA molecular regulation in different plant abiotic stresses. PASmiR currently includes data from ~200 published studies, representing 1038 regulatory relationships between 682 miRNAs and 35 abiotic stresses in 33 plant species. PASmiR’s interface allows users to retrieve miRNA-stress regulatory entries by keyword search using plant species, abiotic stress, and miRNA identifier. Each entry upon keyword query contains detailed regulation information for a specific miRNA, including species name, miRNA identifier, stress name, miRNA expression pattern, detection method for miRNA expression, a reference literature, and target gene(s) of the miRNA extracted from the corresponding reference or miRBase. Users can also contribute novel regulatory entries by using a web-based submission page. The PASmiR database is freely accessible from the two URLs of http://hi.ustc.edu.cn:8080/PASmiR, and http://pcsb.ahau.edu.cn:8080/PASmiR.ConclusionThe PASmiR database provides a solid platform for collection, standardization, and searching of miRNA-abiotic stress regulation data in plants. As such this database will be a comprehensive repository for miRNA regulatory mechanisms involved in plant response to abiotic stresses for the plant stress physiology community.
Insect pests are a major element influencing agricultural production. According to the Food and Agriculture Organization (FAO), an estimated 20–40% of pest damage occurs each year, which reduces global production and becomes a major challenge to crop production. These insect pests cause sooty mold disease by sucking the sap from the crop’s organs, especially leaves, fruits, stems, and roots. To control these pests, pesticides are frequently used because they are fast-acting and scalable. Due to environmental pollution and health awareness, less use of pesticides is recommended. One of the salient approaches could be to reduce the wide use of pesticides by spraying on demand. To perform spot spraying, the location of the pest must first be determined. Therefore, the growing population and increasing food demand emphasize the development of novel methods and systems for agricultural production to address environmental concerns and ensure efficiency and sustainability. To accurately identify these insect pests at an early stage, insect pest detection and classification have recently become in high demand. Thus, this study aims to develop an object recognition system for the detection of crops damaging insect pests and their classification. The current work proposes an automatic system in the form of a smartphone IP- camera to detect insect pests from digital images/videos to reduce farmers’ reliance on pesticides. The proposed approach is based on YOLO object detection architectures including YOLOv5 (n, s, m, l, and x), YOLOv3, YOLO-Lite, and YOLOR. For this purpose, we collected 7046 images in the wild under different illumination and background conditions to train the underlying object detection approaches. We trained and test the object recognition system with different parameters from scratch. The eight models are compared and analyzed. The experimental results show that the average precision (AP@0.5) of the eight models including YOLO-Lite, YOLOv3, YOLOR, and YOLOv5 with five different scales (n, s, m, l, and x) reach 51.7%, 97.6%, 96.80%, 83.85%, 94.61%, 97.18%, 97.04%, and 98.3% respectively. The larger the model, the higher the average accuracy of the detection validation results. We observed that the YOLOv5x model is fully functional and can correctly identify the twenty-three species of insect pests at 40.5 milliseconds (ms). The developed model YOLOv5x performs the state-of-the-art model with an average precision value of (mAP@0.5) 98.3%, (mAP@0.5:0.95) value of 79.8%, precision of 94.5% and a recall of 97.8%, and F1-score with 96% on our IP-23 dataset. The results show that the system works efficiently and was able to correctly detect and identify insect pests, which can be employed for realistic application while farming.
Background Essential Proteins are demonstrated to exert vital functions on cellular processes and are indispensable for the survival and reproduction of the organism. Traditional centrality methods perform poorly on complex protein–protein interaction (PPI) networks. Machine learning approaches based on high-throughput data lack the exploitation of the temporal and spatial dimensions of biological information. Results We put forward a deep learning framework to predict essential proteins by integrating features obtained from the PPI network, subcellular localization, and gene expression profiles. In our model, the node2vec method is applied to learn continuous feature representations for proteins in the PPI network, which capture the diversity of connectivity patterns in the network. The concept of depthwise separable convolution is employed on gene expression profiles to extract properties and observe the trends of gene expression over time under different experimental conditions. Subcellular localization information is mapped into a long one-dimensional vector to capture its characteristics. Additionally, we use a sampling method to mitigate the impact of imbalanced learning when training the model. With experiments carried out on the data of Saccharomyces cerevisiae, results show that our model outperforms traditional centrality methods and machine learning methods. Likewise, the comparative experiments have manifested that our process of various biological information is preferable. Conclusions Our proposed deep learning framework effectively identifies essential proteins by integrating multiple biological data, proving a broader selection of subcellular localization information significantly improves the results of prediction and depthwise separable convolution implemented on gene expression profiles enhances the performance.
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