Computational discovery of microRNAs (miRNA) is based on pre-determined sets of features from miRNA precursors (pre-miRNA). Some feature sets are composed of sequence-structure patterns commonly found in pre-miRNAs, while others are a combination of more sophisticated RNA features. In this work, we analyze the discriminant power of seven feature sets, which are used in six pre-miRNA prediction tools. The analysis is based on the classification performance achieved with these feature sets for the training algorithms used in these tools. We also evaluate feature discrimination through the F-score and feature importance in the induction of random forests.

Seed coat characteristics may be related to seed quality and longevity, attracting the interest of breeding programs. This study aimed to evaluate the relationship between the water absorption parameters and storage tolerance of soybean seeds with contrasting seed coat characteristics. For this purpose, seeds of five soybean cultivars with different seed coat colors and lignin contents were used. Before storage, the seed coat lignin content, moisture content, water absorption rate in 11 hydration periods (1, 2, 3, 4, 5, 6, 7, 8, 24, 32, and 48 hours), hydration speed index, germination, viability, and seed vigor were determined. After six months of storage in a dry and cold chamber (at 11ºC and 54% relative humidity [RH]) and uncontrolled environment (at 25ºC and 71% RH), the seeds were evaluated for germination, viability, and vigor to quantify changes in their physiological quality during storage and relate them to the seeds water absorption parameters for the different cultivars. The seed coat lignin content is negatively correlated with the seeds water absorption parameters. Soybean cultivars have different storage tolerance levels. Seeds that absorb larger amounts of water have lower tolerance to deterioration related to temperature and relative humidity fluctuations that occur in storage under uncontrolled conditions, negatively affecting the physiological potential of seeds.

The delineation of management zones is one of the ways to enable the spatially differentiated management of plots using precision agriculture tools. Over the years, the spatial variability of data collected from soil and plant sampling started to be replaced by data collected by proximal and orbital sensors. As a result, the variety and volume of data have increased considerably, making it necessary to use advanced computational tools, such as machine learning, for data analysis and decision-making support. This paper presents a methodology used to establish management zones (MZ) in precision agriculture by analyzing data obtained from soil sampling, proximal sensors and orbital sensors, in experiments carried out in four plots featuring soybean–cotton and soybean–corn crops, in Mato Grosso and Paraná states, Brazil. Four procedures were evaluated, using different input data sets for the MZ delineation: (I) soil attributes, including clay content, apparent electrical conductivity or fertility, along with elevation, yield maps and vegetation indices (VIs) captured during the peak crop biomass period; (II) soil attributes in conjunction with VIs demonstrating strong correlations; (III) solely VIs exhibiting robust correlation with soil attributes and yield; (IV) VIs selected via random forests to identify the importance of the variable for estimating yield. The results showed that the VIs derived from satellite images could effectively replace other types of data. For plots where the natural spatial variability can be easily identified, all procedures favor obtaining MZ maps that allow reductions of 40% to 70% in yield variance, justifying their use. On the other hand, in plots with low natural spatial variability and that do not have reliable yield maps, different data sets used as input do not help in obtaining feasible MZ maps. For areas where anthropogenic activities with spatially differentiated treatment are already present, the exclusive use of VIs for the delineation of MZs must be carried out with reservations.

Background: Discovery of microRNAs (miRNAs) relies on predictive models for characteristic features from miRNA precursors (pre-miRNAs). The short length of miRNA genes and the lack of pronounced sequence features complicate this task. To accommodate the peculiarities of plant and animal miRNAs systems, tools for both systems have evolved differently. However, these tools are biased towards the species for which they were primarily developed and, consequently, their predictive performance on data sets from other species of the same kingdom might be lower. While these biases are intrinsic to the species, their characterization can lead to computational approaches capable of diminishing their negative effect on the accuracy of pre-miRNAs predictive models. We investigate in this study how 45 predictive models induced for data sets from 45 species, distributed in eight subphyla/classes, perform when applied to a species different from the species used in its induction. Results: Our computational experiments show that the separability of pre-miRNAs and pseudo pre-miRNAs instances is species-dependent and no feature set performs well for all species, even within the same subphylum/class. Mitigating this species dependency, we show that an ensemble of classifiers reduced the classification errors for all 45 species. As the ensemble members were obtained using meaningful, and yet computationally viable feature sets, the ensembles also have a lower computational cost than individual classifiers that rely on energy stability parameters, which are of prohibitive computational cost in large scale applications. Conclusion: In this study, the combination of multiple pre-miRNAs feature sets and multiple learning biases enhanced the predictive accuracy of pre-miRNAs classifiers of 45 species. This is certainly a promising approach to be incorporated in miRNA discovery tools towards more accurate and less species-dependent tools. The material to reproduce the results from this paper can be downloaded from http://dx.doi.org/10.5281/zenodo.49754.

Yield maps from combine harvesters are essential in precision agriculture for capturing within-field variability and guiding variable-rate input management. However, in large-scale systems such as those in the Brazilian Cerrado, these maps are often inconsistent due to calibration errors, use of multiple harvesters, and complex post-processing. Orbital remote sensing offers an alternative by providing consistent vegetation index (VI) data for crop monitoring and yield estimation. This study developed regression models relating Sentinel-2 VIs (EVI, TVI, NDVI, and NDRE) to cotton yield data obtained from combine harvesters across 30 commercial plots in Mato Grosso, Brazil, over six cropping seasons (2019–2024), totaling 76 plot-season datasets. Vegetation indices were grouped into 15-day intervals based on days after sowing, and a logistic growth function was applied in the regression modeling. Model performance evaluated using 15 independent plot-seasons showed good pixel-level accuracy, with RMSE of 0.695 t ha⁻¹ and R² of 0.78, with EVI performing slightly better. At the plot scale, mean yield predictions across all datasets achieved an RMSE of 0.41 t ha⁻¹, reflecting the higher reliability of module-based yield measurements. These results demonstrate the potential of Sentinel-2 VIs combined with logistic regression to predict cotton yields in the Cerrado, complementing or replacing harvester-based monitoring.