Dynamic UAV Phenotyping for Rice Disease Resistance Analysis Based on Multisource Data.

Bacterial blight poses a threat to rice production and food security, which can be controlled through large-scale breeding efforts toward resistant cultivars. Unmanned aerial vehicle (UAV) remote sensing provides an alternative means for the infield phenotype evaluation of crop disease resistance to relatively time-consuming and laborious traditional methods. However, the quality of data acquired by UAV can be affected by several factors such as weather, crop growth period, and geographical location, which can limit their utility for the detection of crop disease and resistant phenotypes. Therefore, a more effective use of UAV data for crop disease phenotype analysis is required. In this paper, we used time series UAV remote sensing data together with accumulated temperature data to train the rice bacterial blight severity evaluation model. The best results obtained with the predictive model showed an R p 2 of 0.86 with an RMSEp of 0.65. Moreover, model updating strategy was used to explore the scalability of the established model in different geographical locations. Twenty percent of transferred data for model training was useful for the evaluation of disease severity over different sites. In addition, the method for phenotypic analysis of rice disease we built here was combined with quantitative trait loci (QTL) analysis to identify resistance QTL in genetic populations at different growth stages. Three new QTLs were identified, and QTLs identified at different growth stages were inconsistent. QTL analysis combined with UAV high-throughput phenotyping provides new ideas for accelerating disease resistance breeding.

Evaluation of rice bacterial blight severity from lab to field with hyperspectral imaging technique.

Hyperspectral imaging technique combined with machine learning is a powerful tool for the evaluation of disease phenotype in rice disease-resistant breeding. However, the current studies are almost carried out in the lab environment, which is difficult to apply to the field environment. In this paper, we used visible/near-infrared hyperspectral images to analysis the severity of rice bacterial blight (BB) and proposed a novel disease index construction strategy (NDSCI) for field application. A designed long short-term memory network with attention mechanism could evaluate the BB severity robustly, and the attention block could filter important wavelengths. Best results were obtained based on the fusion of important wavelengths and color features with an accuracy of 0.94. Then, NSDCI was constructed based on the important wavelength and color feature related to BB severity. The correlation coefficient of NDSCI extended to the field data reached -0.84, showing good scalability. This work overcomes the limitations of environmental conditions and sheds new light on the rapid measurement of phenotype in disease-resistant breeding.

End-to-End Fusion of Hyperspectral and Chlorophyll Fluorescence Imaging to Identify Rice Stresses.

Herbicides and heavy metals are hazardous substances of environmental pollution, resulting in plant stress and harming humans and animals. Identification of stress types can help trace stress sources, manage plant growth, and improve stress-resistant breeding. In this research, hyperspectral imaging (HSI) and chlorophyll fluorescence imaging (Chl-FI) were adopted to identify the rice plants under two types of herbicide stresses (butachlor (DCA) and quinclorac (ELK)) and two types of heavy metal stresses (cadmium (Cd) and copper (Cu)). Visible/near-infrared spectra of leaves (L-VIS/NIR) and stems (S-VIS/NIR) extracted from HSI and chlorophyll fluorescence kinetic curves of leaves (L-Chl-FKC) and stems (S-Chl-FKC) extracted from Chl-FI were fused to establish the models to detect the stress of the hazardous substances. Novel end-to-end deep fusion models were proposed for low-level, middle-level, and high-level information fusion to improve identification accuracy. Results showed that the high-level fusion-based convolutional neural network (CNN) models reached the highest detection accuracy (97.7%), outperforming the models using a single data source (<94.7%). Furthermore, the proposed end-to-end deep fusion models required a much simpler training procedure than the conventional two-stage deep learning fusion. This research provided an efficient alternative for plant stress phenotyping, including identifying plant stresses caused by hazardous substances of environmental pollution.

Combination of spectral index and transfer learning strategy for glyphosate-resistant cultivar identification.

Glyphosate is one of the most widely used non-selective herbicides, and the creation of glyphosate-resistant cultivars solves the problem of limited spraying area. Therefore, it is of great significance to quickly identify resistant cultivars without destruction during the development of superior cultivars. This work took maize seedlings as the experimental object, and the spectral indices of leaves were calculated to construct a model with good robustness that could be used in different experiments. Compared with no transfer strategies, transferability of support vector machine learning model was improved by randomly selecting 14% of source domain from target domain to train and applying transfer component analysis algorithm, the accuracy on target domain reached 83% (increased by 71%), recall increased from 10 to 100%, and F1-score increased from 0.17 to 0.86. The overall results showed that both transfer component analysis algorithm and updating source domain could improve the transferability of model among experiments, and these two transfer strategies could complement each other's advantages to achieve the best classification performance. Therefore, this work is beneficial to timely understanding of the physiological status of plants, identifying glyphosate resistant cultivars, and ultimately provides theoretical basis and technical support for new cultivar creation and high-throughput selection.

Advanced high-throughput plant phenotyping techniques for genome-wide association studies: A review.

Linking phenotypes and genotypes to identify genetic architectures that regulate important traits is crucial for plant breeding and the development of plant genomics. In recent years, genome-wide association studies (GWASs) have been applied extensively to interpret relationships between genes and traits. Successful GWAS application requires comprehensive genomic and phenotypic data from large populations. Although multiple high-throughput DNA sequencing approaches are available for the generation of genomics data, the capacity to generate high-quality phenotypic data is lagging far behind. Traditional methods for plant phenotyping mostly rely on manual measurements, which are laborious, inaccurate, and time-consuming, greatly impairing the acquisition of phenotypic data from large populations. In contrast, high-throughput phenotyping has unique advantages, facilitating rapid, non-destructive, and high-throughput detection, and, in turn, addressing the shortcomings of traditional methods. Aim of Review: This review summarizes the current status with regard to the integration of high-throughput phenotyping and GWAS in plants, in addition to discussing the inherent challenges and future prospects. Key Scientific Concepts of Review: High-throughput phenotyping, which facilitates non-contact and dynamic measurements, has the potential to offer high-quality trait data for GWAS and, in turn, to enhance the unraveling of genetic structures of complex plant traits. In conclusion, high-throughput phenotyping integration with GWAS could facilitate the revealing of coding information in plant genomes.

Recent progress of nondestructive techniques for fruits damage inspection: a review.

In the process of growing, harvesting, and storage, fruits are vulnerable to mechanical damage, microbial infections, and other types of damage, which not only reduce the quality of fruits, increase the risk of fungal infections, in turn greatly affect food safety, but also sharply reduce economic benefits. Hence, it is essential to identify damaged fruits in time. Rapid and nondestructive detection of fruits damage is in great demand. In this paper, the latest research progresses on the detection of fruits damage by nondestructive techniques, including visible/near-infrared spectroscopy, chlorophyll fluorescence techniques, computer vision, multispectral and hyperspectral imaging, structured-illumination reflectance imaging, laser-induced backscattering imaging, optical coherence tomography, nuclear magnetic resonance and imaging, X-ray imaging, electronic nose, thermography, and acoustic methods, are summarized. We briefly introduce the principles of these techniques, summarize their applicability. The challenges and future trends are also proposed to provide beneficial reference for future researches and real-world applications.

Detection of adulteration in food based on nondestructive analysis techniques: a review.

In recent years, people pay more and more attention to food quality and safety, which are significantly relating to human health. Food adulteration is a world-wide concerned issue relating to food quality and safety, and it is difficult to be detected. Modern detection techniques (high performance liquid chromatography, gas chromatography-mass spectrometer, etc.) can accurately identify the types and concentrations of adulterants in different food types. However, the characteristics as expensive, low efficient and complex sample preparation and operation limit the use of these techniques. The rapid, nondestructive and accurate detection techniques of food adulteration is of great and urgent demand. This paper introduced the principles, advantages and disadvantages of the nondestructive analysis techniques and reviewed the applications of these techniques in food adulteration screen in recent years. Differences among these techniques, differences on data interpretation and future prospects were also discussed.

Associations of estimated 24-h urinary sodium excretion with mortality and cardiovascular events in Chinese adults: a prospective cohort study.

OBJECTIVE: To investigate the associations of sodium excretion with blood pressure, mortality and cardiovascular diseases in Chinese population. METHODS: We studied 39 366 individuals aged 35-70 years from 115 urban and rural communities in 12 centers across mainland China. Trained research staff conducted face-to-face interview to record baseline information of all participants based on questionnaires, and collected their morning fasting urine samples to estimate 24-h sodium excretion (24hUNaE). Multivariable frailty Cox regression accounting for clustering by centre was performed to examine the association between estimated 24hUNaE and the primary composite outcome of death and major cardiovascular events in a Chinese population. RESULTS: Mean 24hUNaE was 5.68 (SD 1.69) g/day. After a median follow-up of 8.8 years, the composite outcome occurred in 3080 (7.8%) participants, of which 1426 (3.5%) died and 2192 (5.4%) suffered from cardiovascular events. 24hUNaE was positively associated with increased SBP and DBP. Using the 24hUNaE level of 4-4.99 g/day as the reference group, a 24hUNaE of either lower (<3 g/day) or higher (≥7 g/day) was associated with an increased risk of the composite outcome with a hazard ratio of 1.22 (95% confidence interval: 1.01-1.49) and 1.15 (95% confidence interval: 1.01-1.30), respectively. A similar trend was observed between 24hUNaE level and risk of death or major cardiovascular events. CONCLUSION: These findings support a positive association between estimated urinary sodium excretion and blood pressure, and a possible J-shaped pattern of association between sodium excretion and clinical outcomes, with the lowest risk in participants with sodium excretion between 3 and 5 g/day.

Application of Convolutional Neural Network-Based Feature Extraction and Data Fusion for Geographical Origin Identification of Radix Astragali by Visible/Short-Wave Near-Infrared and Near Infrared Hyperspectral Imaging.

Radix Astragali is a prized traditional Chinese functional food that is used for both medicine and food purposes, with various benefits such as immunomodulation, anti-tumor, and anti-oxidation. The geographical origin of Radix Astragali has a significant impact on its quality attributes. Determining the geographical origins of Radix Astragali is essential for quality evaluation. Hyperspectral imaging covering the visible/short-wave near-infrared range (Vis-NIR, 380-1030 nm) and near-infrared range (NIR, 874-1734 nm) were applied to identify Radix Astragali from five different geographical origins. Principal component analysis (PCA) was utilized to form score images to achieve preliminary qualitative identification. PCA and convolutional neural network (CNN) were used for feature extraction. Measurement-level fusion and feature-level fusion were performed on the original spectra at different spectral ranges and the corresponding features. Support vector machine (SVM), logistic regression (LR), and CNN models based on full wavelengths, extracted features, and fusion datasets were established with excellent results; all the models obtained an accuracy of over 98% for different datasets. The results illustrate that hyperspectral imaging combined with CNN and fusion strategy could be an effective method for origin identification of Radix Astragali.

Detection of Sulfite Dioxide Residue on the Surface of Fresh-Cut Potato Slices Using Near-Infrared Hyperspectral Imaging System and Portable Near-Infrared Spectrometer.

Sodium pyrosulfite is a browning inhibitor used for the storage of fresh-cut potato slices. Excessive use of sodium pyrosulfite can lead to sulfur dioxide residue, which is harmful for the human body. The sulfur dioxide residue on the surface of fresh-cut potato slices immersed in different concentrations of sodium pyrosulfite solution was classified by near-infrared hyperspectral imaging (NIR-HSI) system and portable near-infrared (NIR) spectrometer. Principal component analysis was used to analyze the object-wise spectra, and support vector machine (SVM) model was established. The classification accuracy of calibration set and prediction set were 98.75% and 95%, respectively. Savitzky-Golay algorithm was used to recognize the important wavelengths, and SVM model was established based on the recognized important wavelengths. The final classification accuracy was slightly less than that based on the full spectra. In addition, the pixel-wise spectra extracted from NIR-HSI system could realize the visualization of different samples, and intuitively reflect the differences among the samples. The results showed that it was feasible to classify the sulfur dioxide residue on the surface of fresh-cut potato slices immersed in different concentration of sodium pyrosulfite solution by NIR spectra. It provided an alternative method for the detection of sulfur dioxide residue on the surface of fresh-cut potato slices.

Rapid Screen of the Color and Water Content of Fresh-Cut Potato Tuber Slices Using Hyperspectral Imaging Coupled with Multivariate Analysis.

Color index and water content are important indicators for evaluating the quality of fresh-cut potato tuber slices. In this study, hyperspectral imaging combined with multivariate analysis was used to detect the color parameters (L*, a*, b*, Browning index (BI), L*/b*) and water content of fresh-cut potato tuber slices. The successive projections algorithm (SPA) and competitive adaptive reweighted sampling (CARS) were used to extract characteristic wavelengths, partial least squares (PLS) and least squares support vector machine (LS-SVM) were utilized to establish regression models. For color prediction, R2c, R2p and RPD of all the LSSVM models established for the five color indicators L*, a*, b*, BI, L*/b* were exceeding 0.90, 0.84 and 2.1, respectively. For water content prediction, R2c, R2p, and RPD of the LSSVM models were over 0.80, 0.77 and 1.9, respectively. LS-SVM model based on full spectra was used to reappear the spatial distribution of color and water content in fresh-cut potato tuber slices by pseudo-color imaging since it performed best in most cases. The results illustrated that hyperspectral imaging could be an effective method for color and water content prediction, which could provide solid theoretical basis for subsequent grading and processing of fresh-cut potato tuber slices.

Application of near-infrared hyperspectral imaging to identify a variety of silage maize seeds and common maize seeds.

Common maize seeds and silage maize seeds are similar in appearance and are difficult to identify with the naked eye. Four varieties of common maize seeds and four varieties of silage maize seeds were identified by near-infrared hyperspectral imaging (NIR-HSI) combined with chemometrics. The pixel-wise principal component analysis was used to distinguish the differences among different varieties of maize seeds. The object-wise spectra of each single seed sample were extracted to build classification models. Support vector machine (SVM) and radial basis function neural network (RBFNN) classification models were established using two different classification strategies. First, the maize seeds were directly classified into eight varieties with the prediction accuracy of the SVM model and RBFNN model over 86%. Second, the seeds of silage maize and common maize were firstly classified with the classification accuracy over 88%, then the seeds were classified into four varieties, respectively. The classification accuracy of silage maize seeds was over 98%, and the classification accuracy of common maize seeds was over 97%. The results showed that the varieties of common maize seeds and silage maize seeds could be classified by NIR-HSI combined with chemometrics, which provided an effective means to ensure the purity of maize seeds, especially to isolate common seeds and silage seeds.

Discrimination of Chrysanthemum Varieties Using Hyperspectral Imaging Combined with a Deep Convolutional Neural Network.

Rapid and accurate discrimination of Chrysanthemum varieties is very important for producers, consumers and market regulators. The feasibility of using hyperspectral imaging combined with deep convolutional neural network (DCNN) algorithm to identify Chrysanthemum varieties was studied in this paper. Hyperspectral images in the spectral range of 874⁻1734 nm were collected for 11,038 samples of seven varieties. Principal component analysis (PCA) was introduced for qualitative analysis. Score images of the first five PCs were used to explore the differences between different varieties. Second derivative (2nd derivative) method was employed to select optimal wavelengths. Support vector machine (SVM), logistic regression (LR), and DCNN were used to construct discriminant models using full wavelengths and optimal wavelengths. The results showed that all models based on full wavelengths achieved better performance than those based on optimal wavelengths. DCNN based on full wavelengths obtained the best results with an accuracy close to 100% on both training set and testing set. This optimal model was utilized to visualize the classification results. The overall results indicated that hyperspectral imaging combined with DCNN was a very powerful tool for rapid and accurate discrimination of Chrysanthemum varieties. The proposed method exhibited important potential for developing an online Chrysanthemum evaluation system.

Association patterns of urinary sodium, potassium, and their ratio with blood pressure across various levels of salt-diet regions in China.

We aim to evaluate the association of systolic and diastolic blood pressure (SBP and DBP) with estimated urinary sodium (Na) and potassium(K) excretions, and their gram-to-gram Na/K ratio across various salt-diet regions during 2005-2009 in China. A prospective cohort study was conducted to recruit 46,285 participants in China. A single fasting morning urine specimen was collected to estimate 24-hour urinary Na and K excretion using Kawasaki formula. Means of estimated Na and K were 5.7 ± 1.7 and 2.1 ± 0.5 grams/day, respectively, and mean estimated Na/K ratio was 2.8 ± 0.8. Adjusted analyses showed 1.70 mmHg SBP and 0.49 mmHg DBP increase per 1-g increment of estimated Na, while 1.10 mmHg SBP and 0.91 mmHg DBP decrease for one-gram increase of K. A significant increase in SBP (4.33 mmHg) and DBP (1.54 mmHg) per 1 unit increase in Na/K ratio was observed. More changes of SBP (4.39 mmHg) and DBP (1.67 mmHg) per one-unit increase of Na/K ratio were observed in low-salt regions, though significant changes were also found in moderate- and heavy-salt regions (P for heterogeneity < 0.01). Conclusively, decreasing sodium combined with increasing potassium is likely to have a more beneficial effect than decreasing sodium alone, even if those were living in low-salt regions.

Inequalities in the use of secondary prevention of cardiovascular disease by socioeconomic status: evidence from the PURE observational study.

BACKGROUND: There is little evidence on the use of secondary prevention medicines for cardiovascular disease by socioeconomic groups in countries at different levels of economic development. METHODS: We assessed use of antiplatelet, cholesterol, and blood-pressure-lowering drugs in 8492 individuals with self-reported cardiovascular disease from 21 countries enrolled in the Prospective Urban Rural Epidemiology (PURE) study. Defining one or more drugs as a minimal level of secondary prevention, wealth-related inequality was measured using the Wagstaff concentration index, scaled from -1 (pro-poor) to 1 (pro-rich), standardised by age and sex. Correlations between inequalities and national health-related indicators were estimated. FINDINGS: The proportion of patients with cardiovascular disease on three medications ranged from 0% in South Africa (95% CI 0-1·7), Tanzania (0-3·6), and Zimbabwe (0-5·1), to 49·3% in Canada (44·4-54·3). Proportions receiving at least one drug varied from 2·0% (95% CI 0·5-6·9) in Tanzania to 91·4% (86·6-94·6) in Sweden. There was significant (p<0·05) pro-rich inequality in Saudi Arabia, China, Colombia, India, Pakistan, and Zimbabwe. Pro-poor distributions were observed in Sweden, Brazil, Chile, Poland, and the occupied Palestinian territory. The strongest predictors of inequality were public expenditure on health and overall use of secondary prevention medicines. INTERPRETATION: Use of medication for secondary prevention of cardiovascular disease is alarmingly low. In many countries with the lowest use, pro-rich inequality is greatest. Policies associated with an equal or pro-poor distribution include free medications and community health programmes to support adherence to medications. FUNDING: Full funding sources listed at the end of the paper (see Acknowledgments).

Does greater individual social capital improve the management of hypertension? Cross-national analysis of 61 229 individuals in 21 countries.

INTRODUCTION: Social capital, characterised by trust, reciprocity and cooperation, is positively associated with a number of health outcomes. We test the hypothesis that among hypertensive individuals, those with greater social capital are more likely to have their hypertension detected, treated and controlled. METHODS: Cross-sectional data from 21 countries in the Prospective Urban and Rural Epidemiology study were collected covering 61 229 hypertensive individuals aged 35-70 years, their households and the 656 communities in which they live. Outcomes include whether hypertensive participants have their condition detected, treated and/or controlled. Multivariate statistical models adjusting for community fixed effects were used to assess the associations of three social capital measures: (1) membership of any social organisation, (2) trust in other people and (3) trust in organisations, stratified into high-income and low-income country samples. RESULTS: In low-income countries, membership of any social organisation was associated with a 3% greater likelihood of having one's hypertension detected and controlled, while greater trust in organisations significantly increased the likelihood of detection by 4%. These associations were not observed among participants in high-income countries. CONCLUSION: Although the observed associations are modest, some aspects of social capital are associated with better management of hypertension in low-income countries where health systems are often weak. Given that hypertension affects millions in these countries, even modest gains at all points along the treatment pathway could improve management for many, and translate into the prevention of thousands of cardiovascular events each year.

Does greater individual social capital improve the management of hypertension? Cross-national analysis of 61 229 individuals in 21 countries

INTRODUCTION:Social capital, characterised by trust, reciprocity and cooperation, is positively associated with a number of health outcomes. We test the hypothesis that among hypertensive individuals, those with greater social capital are more likely to have their hypertension detected, treated and controlled.METHODS:Cross-sectional data from 21 countries in the Prospective Urban and Rural Epidemiology study were collected covering 61 229 hypertensive individuals aged 35-70 years, their households and the 656 communities in which they live. Outcomes include whether hypertensive participants have their condition detected, treated and/or controlled. Multivariate statistical models adjusting for community fixed effects were used to assess the associations of three social capital measures: (1) membership of any social organisation, (2) trust in other people and (3) trust in organisations, stratified into high-income and low-income country samples.