Cell subtype-specific effects of genetic variation in the Alzheimer's disease brain.

The relationship between genetic variation and gene expression in brain cell types and subtypes remains understudied. Here, we generated single-nucleus RNA sequencing data from the neocortex of 424 individuals of advanced age; we assessed the effect of genetic variants on RNA expression in cis (cis-expression quantitative trait loci) for seven cell types and 64 cell subtypes using 1.5 million transcriptomes. This effort identified 10,004 eGenes at the cell type level and 8,099 eGenes at the cell subtype level. Many eGenes are only detected within cell subtypes. A new variant influences APOE expression only in microglia and is associated with greater cerebral amyloid angiopathy but not Alzheimer's disease pathology, after adjusting for APOEε4, providing mechanistic insights into both pathologies. Furthermore, only a TMEM106B variant affects the proportion of cell subtypes. Integration of these results with genome-wide association studies highlighted the targeted cell type and probable causal gene within Alzheimer's disease, schizophrenia, educational attainment and Parkinson's disease loci.

A Single-Nucleus Transcriptome-Wide Association Study Implicates Novel Genes in Depression Pathogenesis.

BACKGROUND: Depression, a common psychiatric illness and global public health problem, remains poorly understood across different life stages, which hampers the development of novel treatments. METHODS: To identify new candidate genes for therapeutic development, we performed differential gene expression analysis of single-nucleus RNA sequencing data from the dorsolateral prefrontal cortex of older adults (n = 424) in relation to antemortem depressive symptoms. Additionally, we integrated genome-wide association study results for depression (n = 500,199) along with genetic tools for inferring the expression of 14,048 unique genes in 7 cell types and 52 cell subtypes to perform a transcriptome-wide association study of depression followed by Mendelian randomization. RESULTS: Our single-nucleus transcriptome-wide association study analysis identified 68 candidate genes for depression and showed the greatest number being in excitatory and inhibitory neurons. Of the 68 genes, 53 were novel compared to previous studies. Notably, gene expression in different neuronal subtypes had varying effects on depression risk. Traits with high genetic correlations with depression, such as neuroticism, shared more transcriptome-wide association study genes than traits that were not highly correlated with depression. Complementing these analyses, differential gene expression analysis across 52 neocortical cell subtypes showed that genes such as KCNN2, SCAI, WASF3, and SOCS6 were associated with late-life depressive symptoms in specific cell subtypes. CONCLUSIONS: These 2 sets of analyses illustrate the utility of large single-nucleus RNA sequencing data both to uncover genes whose expression is altered in specific cell subtypes in the context of depressive symptoms and to enhance the interpretation of well-powered genome-wide association studies so that we can prioritize specific susceptibility genes for further analysis and therapeutic development.

A single-nucleus transcriptome-wide association study implicates novel genes in depression pathogenesis.

Background: Depression is a common psychiatric illness and global public health problem. However, our limited understanding of the biological basis of depression has hindered the development of novel treatments and interventions. Methods: To identify new candidate genes for therapeutic development, we examined single-nucleus RNA sequencing (snucRNAseq) data from the dorsolateral prefrontal cortex (N=424) in relation to ante-mortem depressive symptoms. To complement these direct analyses, we also used genome-wide association study (GWAS) results for depression (N=500,199) along with genetic tools for inferring the expression of 22,159 genes in 7 cell types and 55 cell subtypes to perform transcriptome-wide association studies (TWAS) of depression followed by Mendelian randomization (MR). Results: Our single-nucleus TWAS analysis identified 71 causal genes in depression that have a role in specific neocortical cell subtypes; 59 of 71 genes were novel compared to previous studies. Depression TWAS genes showed a cell type specific pattern, with the greatest enrichment being in both excitatory and inhibitory neurons as well as astrocytes. Gene expression in different neuron subtypes have different directions of effect on depression risk. Compared to lower genetically correlated traits (e.g. body mass index) with depression, higher correlated traits (e.g., neuroticism) have more common TWAS genes with depression. In parallel, we performed differential gene expression analysis in relation to depression in 55 cortical cell subtypes, and we found that genes such as ANKRD36, MADD, TAOK3, SCAI and CHUK are associated with depression in specific cell subtypes. Conclusions: These two sets of analyses illustrate the utility of large snucRNAseq data to uncover both genes whose expression is altered in specific cell subtypes in the context of depression and to enhance the interpretation of well-powered GWAS so that we can prioritize specific susceptibility genes for further analysis and therapeutic development.

Crop pest image classification based on improved densely connected convolutional network.

Introduction: Crop pests have a great impact on the quality and yield of crops. The use of deep learning for the identification of crop pests is important for crop precise management. Methods: To address the lack of data set and poor classification accuracy in current pest research, a large-scale pest data set named HQIP102 is built and the pest identification model named MADN is proposed. There are some problems with the IP102 large crop pest dataset, such as some pest categories are wrong and pest subjects are missing from the images. In this study, the IP102 data set was carefully filtered to obtain the HQIP102 data set, which contains 47,393 images of 102 pest classes on eight crops. The MADN model improves the representation capability of DenseNet in three aspects. Firstly, the Selective Kernel unit is introduced into the DenseNet model, which can adaptively adjust the size of the receptive field according to the input and capture target objects of different sizes more effectively. Secondly, in order to make the features obey a stable distribution, the Representative Batch Normalization module is used in the DenseNet model. In addition, adaptive selection of whether to activate neurons can improve the performance of the network, for which the ACON activation function is used in the DenseNet model. Finally, the MADN model is constituted by ensemble learning. Results: Experimental results show that MADN achieved an accuracy and F1Score of 75.28% and 65.46% on the HQIP102 data set, an improvement of 5.17 percentage points and 5.20 percentage points compared to the pre-improvement DenseNet-121. Compared with ResNet-101, the accuracy and F1Score of MADN model improved by 10.48 percentage points and 10.56 percentage points, while the parameters size decreased by 35.37%. Deploying models to cloud servers with mobile application provides help in securing crop yield and quality.

Nondestructive measurement of kiwifruit firmness, soluble solid content (SSC), titratable acidity (TA), and sensory quality by vibration spectrum.

Maturity is a key attribute to evaluate the quality and acceptability of fruit products. In this study, the impact method was used for nondestructive measurement of kiwifruit maturity. The fruit was vertically dropped onto an impact plate, and an accelerometer was used to measure the response signal. Then, fruit firmness, soluble solid content (SSC), titratable acidity (TA), and sensory scores were measured to determine the kiwifruit maturity. In addition, different modeling methods were proposed for data analysis. The results showed that the optimized prediction results were obtained by the principal component analysis-back-propagation neural network (PCA-BPNN) method for both quantitative and qualitative analysis. The optimized correlation coefficient between prediction and actual values (r p) and root mean square error of prediction (RESEP) for firmness, SSC, TA, and sensory score were 0.881 (2.359N), 0.641 (1.511 Brix), 0.568 (0.023%), and 0.935 (0.693), respectively. The optimized discriminant accuracy for immature, mature, and overmature kiwifruits was 94.2% and 92.1% for calibration and validation, respectively. Such results indicated the feasibility of the proposed impact method for kiwifruit maturity evaluation.

Application of hyperspectral imaging for spatial prediction of soluble solid content in sweet potato.

Visible and near infrared (Vis-NIR) hyperspectral imaging was used for fast detection and visualization of soluble solid content (SSC) in 'Beijing 553' and 'Red Banana' sweet potatoes. Hyperspectral images were acquired from 420 ROIs of each cultivar of sliced sweet potatoes. There were 8 and 10 outliers removed from 'Beijing 553' and 'Red Banana' sweet potatoes by Monte Carlo partial least squares (MCPLS). The optimal spectral pretreatments were determined to enhance the performance of the prediction model. Successive projections algorithm (SPA) and competitive adaptive reweighted sampling (CARS) were employed to select characteristic wavelengths. SSC prediction models were developed using partial least squares regression (PLSR), support vector regression (SVR) and multivariate linear regression (MLR). The more effective prediction performances emerged from the SPA-SVR model with R p 2 of 0.8581, RMSEP of 0.2951 and RPDp of 2.56 for 'Beijing 553' sweet potato, and the CARS-MLR model with R p 2 of 0.8153, RMSEP of 0.2744 and RPDp of 2.09 for 'Red Banana' sweet potato. Spatial distribution maps of SSC were obtained in a pixel-wise manner using SPA-SVR and CARS-MLR models for quantifying the SSC level in a simple way. The overall results illustrated that Vis-NIR hyperspectral imaging was a powerful tool for spatial prediction of SSC in sweet potatoes.

Determination of the bruise degree for cherry using Vis-NIR reflection spectroscopy coupled with multivariate analysis.

Determination and classification of the bruise degree for cherry can improve consumer satisfaction with cherry quality and enhance the industry's competiveness and profitability. In this study, visible and near infrared (Vis-NIR) reflection spectroscopy was used for identifying bruise degree of cherry in 350-2500 nm. Sampling spectral data were extracted from normal, slight and severe bruise samples. Principal component analysis (PCA) was implemented to determine the first few principal components (PCs) for cluster analysis among samples. Optimal wavelengths were selected by loadings of PCs from PCA and successive projection algorithm (SPA) method, respectively. Afterwards, these optimal wavelengths were empolyed to establish the classification models as inputs of least square-support vector machine (LS-SVM). Better performance for qualitative discrimination of the bruise degree for cherry was emerged in LS-SVM model based on five optimal wavelengths (603, 633, 679, 1083, and 1803 nm) selected directly by SPA, which showed acceptable results with the classification accuracy of 93.3%. Confusion matrix illustrated misclassification generally occurred in normal and slight bruise samples. Furthermore, the latent relation between spectral property of cherries in varying bruise degree and its firmness and soluble solids content (SSC) was analyzed. The result showed both colour, firmness and SSC were consistent with the Vis-NIR reflectance of cherries. Overall, this study revealed that Vis-NIR reflection spectroscopy integrated with multivariate analysis can be used as a rapid, intact method to determine the bruise degree of cherry, laying a foundation for cherry sorting and postharvest quality control.

A Real-Time Weed Mapping and Precision Herbicide Spraying System for Row Crops.

This study developed and field tested an automated weed mapping and variable-rate herbicide spraying (VRHS) system for row crops. Weed detection was performed through a machine vision sub-system that used a custom threshold segmentation method, an improved particle swarm optimum (IPSO) algorithm, capable of segmenting the field images. The VRHS system also used a lateral histogram-based algorithm for fast extraction of weed maps. This was the basis for determining real-time herbicide application rates. The central processor of the VRHS system had high logic operation capacity, compared to the conventional controller-based systems. Custom developed monitoring system allowed real-time visualization of the spraying system functionalities. Integrated system performance was then evaluated through field experiments. The IPSO successfully segmented weeds within corn crop at seedling growth stage and reduced segmentation error rates to 0.1% from 7.1% of traditional particle swarm optimization algorithm. IPSO processing speed was 0.026 s/frame. The weed detection to chemical actuation response time of integrated system was 1.562 s. Overall, VRHS system met the real-time data processing and actuation requirements for its use in practical weed management applications.