An improved EfficientNet model and its applications in pneumonia image classification

Since the outburst of COVID-19, the medical system has been facing great challenges due to the explosive growth in detection and treatment needs within a short period. To improve the working efficiency of doctors, an improved EfficientNet model of Convolutional Neural Network (CNN) was proposed and applied for the diagnosis of pneumonia cases and the classification of relevant images in the present study. First, the acquired images of pneumonia cases were divided to determine the zones with target features, and image size was limited to improve the training speed of the network. Meanwhile, reinforcement learning was performed to the input dataset to further improve the training effect of the model. Second, the preprocessed images were inputted into the improved EfficientNet-B4 model. The depth and width of the model, as well as the resolution of the input images, were determined by optimizing the combination coefficient. On this basis, the model was scaled, and then its ability in extracting the features of deep-layer images was strengthened by introducing the attention mechanism. Third, the learning rate was adjusted by using the Adaptive Momentum (ADAM), and the training efficiency of the model was accelerated. Finally, the test set was inputted into the trained model. Results demonstrate that the improved model could detect 98% of patients with pneumonia and 97% of patients without pneumonia. The accuracy rate, precision rate, and sensitivity of the model were generally improved. Lastly, the training and test results of VGGNet, SqueezeNet-Elus, SqueezeNet-Relu, and the improved EfficientNet-B4 models were compared and evaluated. The improved EfficientNet-B4 model achieved the highest comprehensive accuracy rate, reaching 92.95%. The proposed method provides some references to the application of the CNN model in image classification and recognition

Variations in Growth and Photosynthetic Traits of Polyploid Poplar Hybrids and Clones in Northeast China

To evaluate differences among 19 different ploidy hybrid poplar clones grown in northeast China, 21 traits related to growth traits and photosynthetic characteristics were detected and analyzed. Abundant phenotypic variations exist among and within populations, and these variations are the basis of forest tree genetic improvements. In this research, variance analysis showed that the traits except the net photosynthesis rate among the different ploidies and all the other traits exhibited significant differences among the ploidies or clones (p < 0.01). Estimation of phenotypic coefficients of variation, genotypic coefficients of variation, and repeatability is important for selecting superior materials. The larger the value, the greater the potential for material selection improvement. The repeatability of the different traits ranged from 0.88 to 0.99. The phenotypic and genotypic coefficients of variation of all the investigated traits ranged from 6.88% to 57.40% and from 4.85% to 42.89%, respectively. Correlation analysis showed that there were significant positive correlations between tree height, diameter, and volume. Transpiration rate, intercellular carbon dioxide concentration, and stomatal conductance were significantly positively correlated with each other but negatively correlated with instantaneous water use efficiency. Growth traits were weakly correlated with photosynthetic indexes. The rank correlation coefficient showed that most of the growth indicators reached a significant correlation level among different years (0.40-0.98), except 1-year-old tree height with 4-year-old tree height and 1-year-old ground diameter with 3-year-old tree height, which indicated the potential possibility for early selection of elite clones. Principal analysis results showed that the contribution rate of the first principal component was 46.606%, and 2-year-old tree height, 2-year-old ground diameter, 3-year-old tree height, 3-year-old ground diameter, 3-year-old diameter at breast height, 3-year-old volume, 4-year-old tree height, 4-year-old ground diameter, 4-year-old diameter at breast height, and 4-year-old volume showed higher vector values than other traits. With the method of multiple-trait comprehensive evaluation to evaluate clones, SX3.1, SY3.1, and XY4.2 were selected as elite clones, and the genetic gains of height, basal diameter, diameter at breast height, and volume of selected clones ranged from 12.85% to 64.87% in the fourth growth year. The results showed fundamental information for selecting superior poplar clones, which might provide new materials for the regeneration and improvement of forests in Northeast China

Stress-inducible expression of an F-box gene TaFBA1 from wheat enhanced the drought tolerance in transgenic tobacco plants without impacting growth and development

E3 ligase plays an important role in the response to many environment stresses in plants. In our previous study, constitutive overexpression of an F-box protein gene TaFBA1 driven by 35S promoter improved the drought tolerance in transgenic tobacco plants, but the growth and development in transgenic plants was altered in normal conditions. In this study, we used stress-inducible promoter RD29A instead of 35S promoter, as a results, the stress-inducible transgenic tobacco plants exhibit a similar phenotype with WT plants. However, the drought tolerance of the transgenic plants with stress-inducible expressed TaFBA1 was enhanced. The improved drought tolerance of transgenic plants was indicated by their higher seed germination rate and survival rate, greater biomass and photosynthesis than those of WT under water stress, which may be related to their greater water retention capability and osmotic adjustment. Moreover, the transgenic plants accumulated less reactive oxygen species (ROS), kept lower MDA content and membrane leakage under water stress, which may be related to their higher levels of antioxidant enzyme activity and upregulated gene expression of some antioxidant enzymes. These results suggest that stress induced expression of TaFBA1 confers drought tolerance via the improved water retention and antioxidative compete abilibty. Meanwhile, this stress-inducible expression strategy by RD29A promoter can minimize the unexpectable effects by 35S constitutive promoter on phenotypes of the transgenic plants

Variations in Growth and Photosynthetic Traits of Polyploid Poplar Hybrids and Clones in Northeast China

To evaluate differences among 19 different ploidy hybrid poplar clones grown in northeast China, 21 traits related to growth traits and photosynthetic characteristics were detected and analyzed. Abundant phenotypic variations exist among and within populations, and these variations are the basis of forest tree genetic improvements. In this research, variance analysis showed that the traits except the net photosynthesis rate among the different ploidies and all the other traits exhibited significant differences among the ploidies or clones (p &lt; 0.01). Estimation of phenotypic coefficients of variation, genotypic coefficients of variation, and repeatability is important for selecting superior materials. The larger the value, the greater the potential for material selection improvement. The repeatability of the different traits ranged from 0.88 to 0.99. The phenotypic and genotypic coefficients of variation of all the investigated traits ranged from 6.88% to 57.40% and from 4.85% to 42.89%, respectively. Correlation analysis showed that there were significant positive correlations between tree height, diameter, and volume. Transpiration rate, intercellular carbon dioxide concentration, and stomatal conductance were significantly positively correlated with each other but negatively correlated with instantaneous water use efficiency. Growth traits were weakly correlated with photosynthetic indexes. The rank correlation coefficient showed that most of the growth indicators reached a significant correlation level among different years (0.40&ndash;0.98), except 1-year-old tree height with 4-year-old tree height and 1-year-old ground diameter with 3-year-old tree height, which indicated the potential possibility for early selection of elite clones. Principal analysis results showed that the contribution rate of the first principal component was 46.606%, and 2-year-old tree height, 2-year-old ground diameter, 3-year-old tree height, 3-year-old ground diameter, 3-year-old diameter at breast height, 3-year-old volume, 4-year-old tree height, 4-year-old ground diameter, 4-year-old diameter at breast height, and 4-year-old volume showed higher vector values than other traits. With the method of multiple-trait comprehensive evaluation to evaluate clones, SX3.1, SY3.1, and XY4.2 were selected as elite clones, and the genetic gains of height, basal diameter, diameter at breast height, and volume of selected clones ranged from 12.85% to 64.87% in the fourth growth year. The results showed fundamental information for selecting superior poplar clones, which might provide new materials for the regeneration and improvement of forests in Northeast China

Overexpression of the Wheat Expansin Gene <i>TaEXPA2</i> Improved Seed Production and Drought Tolerance in Transgenic Tobacco Plants

<div><p>Expansins are cell wall proteins that are grouped into two main families, α-expansins and β-expansins, and they are implicated in the control of cell extension via the disruption of hydrogen bonds between cellulose and matrix glucans. <i>TaEXPA2</i> is an α-expansin gene identified in wheat. Based on putative cis-regulatory elements in the <i>TaEXPA2</i> promoter sequence and the expression pattern induced when polyethylene glycol (PEG) is used to mimic water stress, we hypothesized that <i>TaEXPA2</i> is involved in plant drought tolerance and plant development. Through transient expression of <i>35S</i>::<i>TaEXPA2-GFP</i> in onion epidermal cells, TaEXPA2 was localized to the cell wall. Constitutive expression of <i>TaEXPA2</i> in tobacco improved seed production by increasing capsule number, not seed size, without having any effect on plant growth patterns. The transgenic tobacco exhibited a significantly greater tolerance to water-deficiency stress than did wild-type (WT) plants. We found that under drought stress, the transgenic plants maintained a better water status. The accumulated content of osmotic adjustment substances, such as proline, in <i>TaEXPA2</i> transgenic plants was greater than that in WT plants. Transgenic plants also displayed greater antioxidative competence as indicated by their lower malondialdehyde (MDA) content, relative electrical conductivity, and reactive oxygen species (ROS) accumulation than did WT plants. This result suggests that the transgenic plants suffer less damage from ROS under drought conditions. The activities of some antioxidant enzymes as well as expression levels of several genes encoding key antioxidant enzymes were higher in the transgenic plants than in the WT plants under drought stress. Collectively, our results suggest that ectopic expression of the wheat expansin gene <i>TaEXPA2</i> improves seed production and drought tolerance in transgenic tobacco plants.</p></div

Subcellular localization of the TaEXPA2-GFP protein in onion epidermal cells.

<p>The transient expression of <i>35S</i>::<i>GFP</i> and <i>35S</i>::<i>TaEXPA2-GFP</i> in onion epidermal cells. The cells were analyzed by laser confocal microscopy after culture on MS medium at 28°C for 2 days. Onion cell plasmolysis was induced by a 30% sucrose solution for 20 min before observation.</p

Transcriptomics Profiling of Acer pseudosieboldianum Molecular Mechanism against Freezing Stress

Low temperature is an important environmental factor that affects the growth and development of trees and leads to the introduction of failure in the genetic improvement of trees. Acer pseudosieboldianum is a tree species that is well-known for its bright red autumn leaf color. These trees are widely used in landscaping in northeast China. However, due to their poor cold resistance, introduced A. pseudosieboldianum trees suffer severe freezing injury in many introduced environments. To elucidate the physiological indicators and molecular mechanisms associated with freezing damage, we analyzed the physiological indicators and transcriptome of A. pseudosieboldianum, using kits and RNA-Seq technology. The mechanism of A. pseudosieboldianum in response to freezing stress is an important scientific question. In this study, we used the shoots of four-year-old A. pseudosieboldianum twig seedlings, and the physiological index and the transcriptome of A. pseudosieboldianum under low temperature stress were investigated. The results showed that more than 20,000 genes were detected in A. pseudosieboldianum under low temperature (4 &deg;C) and freezing temperatures (&minus;10 &deg;C, &minus;20 &deg;C, &minus;30 &deg;C, and &minus;40 &deg;C). There were 2505, 6021, 5125, and 3191 differential genes (DEGs) between &minus;10 &deg;C, &minus;20&deg;C, &minus;30&deg;C, &minus;40 &deg;C, and CK (4 &deg;C), respectively. Among these differential genes, 48 genes are involved in the MAPK pathway and 533 genes are involved in the glucose metabolism pathway. In addition, the important transcription factors (MYB, AP2/ERF, and WRKY) involved in freezing stress were activated under different degrees of freezing stress. A total of 10 sets of physiological indicators of A. pseudosieboldianum were examined, including the activities of five enzymes and the accumulation of five hormones. All of the physiological indicators except SOD and GSH-Px reached their maximum values at &minus;30 &deg;C. The enzyme activity of SOD was highest at &minus;10 &deg;C, and that of GSH-Px was highest at &minus;20 &deg;C. Our study is the first to provide a more comprehensive understanding of the differential genes (DEGs) involved in A. pseudosieboldianum under freezing stress at different temperatures at the transcriptome level. These results may help to clarify the molecular mechanism of cold tolerance of A. pseudosieboldianum and provide new insights and candidate genes for the genetic improvement of the freezing tolerance of A. pseudosieboldianum

The expression of antioxidant-related genes in WT and transgenic tobacco plants under drought stress, as detected by qPCR.

<p>The transcript levels of these genes in transgenic plants are indicated relative to the levels in WT plants (taken as 1), and using transcripts of <i>actin</i> in the same samples as a reference. Each column represents the mean ± standard error of three replicates. * and ** indicate significant differences from the WT values at P < 0.05 and P < 0.01, respectively, according to Duncan’s multiple range test.</p

Evaluation of the drought tolerance of <i>TaEXPA2</i> transgenic tobacco plants.

<p>(A) 10-day-old WT and transgenic plants were exposed to natural drought stress for 7 days and re-watered for 2 days, and (B) the corresponding survival rate of transgenic plants after drought stress and re-watering. (C) 50-day-old WT and transgenic plants were naturally exposed to drought for 21 days with the well-watered plants as controls. (D) The corresponding root growth status from (C). (E) Chlorophyll content (mg/g FW). (F) Net photosynthetic rate (Pn, μmol CO₂ m^-2 s^-1). (G) Transpiration rate (E, mmol H₂O m^-2 s^-1). (H) Leaf stomatal conductance (Gs, mmol H₂O m^-2 s^-1). The experiment was replicated three times, and bars indicate SEs. * and ** indicate significant differences of P < 0.05 and P < 0.01, respectively, according to Duncan’s multiple range test.</p

Seed production of WT and <i>TaEXPA2</i> transgenic lines.

<p>(A) Phenotypic comparison of WT and <i>TaEXPA2</i> transgenic lines in the flowering stage. (B) The spike and capsules. (C) Total number of capsules per tobacco plant. (D) Distribution statistics of capsule length. (E) Seed yield of individual tobacco plants. (F) Total seed weight per tobacco plant. Data in (C), (D), and (F) represent the mean values for the six independent biological replicates. In (C) and (F), * and ** indicate significant differences from the WT values at P < 0.05 and P < 0.01, respectively, according to Duncan’s multiple range test.</p