Early Detection of Wild Rocket Tracheofusariosis Using Hyperspectral Image-Based Machine Learning

Fusarium oxysporum f. sp. raphani is responsible for wilting wild rocket (Diplotaxis tenuifolia L. [D.C.]). A machine learning model based on hyperspectral data was constructed to monitor disease progression. Thus, pathogenesis after artificial inoculation was monitored over a 15-day period by symptom assessment, qPCR pathogen quantification, and hyperspectral imaging. The host colonization by a pathogen evolved accordingly with symptoms as confirmed by qPCR. Spectral data showed differences as early as 5-day post infection and 12 hypespectral vegetation indices were selected to follow disease development. The hyperspectral dataset was used to feed the XGBoost machine learning algorithm with the aim of developing a model that discriminates between healthy and infected plants during the time. The multiple cross-prediction strategy of the pixel-level models was able to detect hyperspectral disease profiles with an average accuracy of 0.8. For healthy pixel detection, the mean Precision value was 0.78, the Recall was 0.88, and the F1 Score was 0.82. For infected pixel detection, the average evaluation metrics were Precision: 0.73, Recall: 0.57, and F1 Score: 0.63. Machine learning paves the way for automatic early detection of infected plants, even a few days after infection.

Insect Protein Content Analysis in Handcrafted Fitness Bars by NIR Spectroscopy. Gaussian Process Regression and Data Fusion for Performance Enhancement of Miniaturized Cost-Effective Consumer-Grade Sensors

Future food supply will become increasingly dependent on edible material extracted from insects. The growing popularity of artisanal food products enhanced by insect proteins creates particular needs for establishing effective methods for quality control. This study focuses on developing rapid and efficient on-site quantitative analysis of protein content in handcrafted insect bars by miniaturized near-infrared (NIR) spectrometers. Benchtop (Büchi NIRFlex N-500) and three miniaturized (MicroNIR 1700 ES, Tellspec Enterprise Sensor and SCiO Sensor) in hyphenation to partial least squares regression (PLSR) and Gaussian process regression (GPR) calibration methods and data fusion concept were evaluated via test-set validation in performance of protein content analysis. These NIR spectrometers markedly differ by technical principles, operational characteristics and cost-effectiveness. In the non-destructive analysis of intact bars, the root mean square error of cross prediction (RMSEP) values were 0.611% (benchtop) and 0.545–0.659% (miniaturized) with PLSR, and 0.506% (benchtop) and 0.482–0.580% (miniaturized) with GPR calibration, while the analyzed total protein content was 19.3–23.0%. For milled samples, with PLSR the RMSEP values improved to 0.210% for benchtop spectrometer but remained in the inferior range of 0.525–0.571% for the miniaturized ones. GPR calibration improved the predictive performance of the miniaturized spectrometers, with RMSEP values of 0.230% (MicroNIR 1700 ES), 0.326% (Tellspec) and 0.338% (SCiO). Furthermore, Tellspec and SCiO sensors are consumer-oriented devices, and their combined use for enhanced performance remains a viable economical choice. With GPR calibration and test-set validation performed for fused (Tellspec + SCiO) data, the RMSEP values were improved to 0.517% (in the analysis of intact samples) and 0.295% (for milled samples).

Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning

Experimental studies of Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are essential or non-essential for survival in each species. Recently, a range of features linked to gene essentiality have been inferred using a machine learning (ML)-based approach, allowing essentiality predictions within a species. Nevertheless, predictions between species are still elusive. Here, we undertake a comprehensive study using ML to discover and validate features of essential genes common to both C. elegans and D. melanogaster. We demonstrate that the cross-species prediction of gene essentiality is possible using a subset of features linked to nucleotide/protein sequences, protein orthology and subcellular localisation, single-cell RNA-seq, and histone methylation markers. Complementary analyses showed that essential genes are enriched for transcription and translation functions and are preferentially located away from heterochromatin regions of C. elegans and D. melanogaster chromosomes. The present work should enable the cross-prediction of essential genes between model and non-model metazoans.

Satellite-based estimation of roughness lengths and displacement heights for wind resource modelling

Wind turbines in northern Europe are frequently placed in forests, which sets new wind resource modelling requirements. Accurate mapping of the land surface can be challenging at forested sites due to sudden transitions between patches with very different aerodynamic properties, e.g. tall trees, clearings, and lakes. Tree growth and deforestation can lead to temporal changes of the forest. Global or pan-European land cover data sets fail to resolve these forest properties, aerial lidar campaigns are costly and infrequent, and hand-digitization is labour-intensive and subjective. Here, we investigate the potential of using satellite observations to characterise the land surface in connection with wind energy flow modelling using the Wind Atlas Analysis and Application Program (WAsP). Collocated maps of the land cover, tree height, and Leaf Area Index (LAI) have been generated based on observations from the Sentinel-1 and -2 missions combined with the Ice, Cloud, and Land Elevation Satellite-2 (ICESat-2). Three different forest canopy models are applied to convert these maps to roughness lengths and displacement heights. We introduce a modified model, which can process detailed land cover maps containing both roughness lengths and displacement heights. Extensive validation is carried out through cross-prediction analyses at ten well-instrumented sites in various landscapes. We demonstrate that using the novel satellite-based input maps leads to lower cross-prediction errors of the wind power density than land cover databases at a coarser spatial resolution. Differences in the cross-predictions resulting from the three different canopy models are minor. The satellite-based maps show cross-prediction errors close to those obtained from aerial lidar scans and hand-digitised maps. This demonstrates the value of using detailed satellite-based land cover maps for micro-scale flow modelling.

PROBselect: accurate prediction of protein-binding residues from proteins sequences via dynamic predictor selection

Motivation Knowledge of protein-binding residues (PBRs) improves our understanding of protein−protein interactions, contributes to the prediction of protein functions and facilitates protein−protein docking calculations. While many sequence-based predictors of PBRs were published, they offer modest levels of predictive performance and most of them cross-predict residues that interact with other partners. One unexplored option to improve the predictive quality is to design consensus predictors that combine results produced by multiple methods. Results We empirically investigate predictive performance of a representative set of nine predictors of PBRs. We report substantial differences in predictive quality when these methods are used to predict individual proteins, which contrast with the dataset-level benchmarks that are currently used to assess and compare these methods. Our analysis provides new insights for the cross-prediction concern, dissects complementarity between predictors and demonstrates that predictive performance of the top methods depends on unique characteristics of the input protein sequence. Using these insights, we developed PROBselect, first-of-its-kind consensus predictor of PBRs. Our design is based on the dynamic predictor selection at the protein level, where the selection relies on regression-based models that accurately estimate predictive performance of selected predictors directly from the sequence. Empirical assessment using a low-similarity test dataset shows that PROBselect provides significantly improved predictive quality when compared with the current predictors and conventional consensuses that combine residue-level predictions. Moreover, PROBselect informs the users about the expected predictive quality for the prediction generated from a given input protein. Availability and implementation PROBselect is available at http://bioinformatics.csu.edu.cn/PROBselect/home/index. Supplementary information Supplementary data are available at Bioinformatics online.

Consistent habitat preference underpins the geographically divergent autumn migration of individual Mongolian common shelducks

While many avian populations follow narrow, well-defined “migratory corridors,” individuals from other populations undertake highly divergent individual migration routes, using widely dispersed stopover sites en route between breeding and wintering areas, although the reasons for these differences are rarely investigated. We combined individual GPS-tracked migration data from Mongolian-breeding common shelduck Tadorna tadorna and remote sensing datasets, to investigate habitat selection at inland stopover sites used by these birds during dispersed autumn migration, to explain their divergent migration patterns. We used generalized linear mixed models to investigate population-level resource selection, and generalized linear models to investigate stopover-site-level resource selection. The population-level model showed that water recurrence had the strongest positive effect on determining birds’ occupancy at staging sites, while cultivated land and grassland land cover type had strongest negative effects; effects of other land cover types were negative but weaker, particularly effects of water seasonality and presence of a human footprint, which were positive but weak or non-significant, respectively. Although stopover-site-level models showed variable resource selection patterns, the variance partitioning and cross-prediction AUC scores corroborated high inter-individual consistency in habitat selection at inland stopover sites during the dispersed autumn migration. These results suggest that the geographically widespread distribution (and generally rarity) of suitable habitats explained the spatially divergent autumn migrations of Mongolian breeding common shelduck, rather than the species showing flexible autumn staging habitat occupancy.