ENGEP: advancing spatial transcriptomics with accurate unmeasured gene expression prediction.

Imaging-based spatial transcriptomics techniques provide valuable spatial and gene expression information at single-cell resolution. However, their current capability is restricted to profiling a limited number of genes per sample, resulting in most of the transcriptome remaining unmeasured. To overcome this challenge, we develop ENGEP, an ensemble learning-based tool that predicts unmeasured gene expression in spatial transcriptomics data by using multiple single-cell RNA sequencing datasets as references. ENGEP outperforms current state-of-the-art tools and brings biological insight by accurately predicting unmeasured genes. ENGEP has exceptional efficiency in terms of runtime and memory usage, making it scalable for analyzing large datasets.

[Regulation Control of a Tribasic Amendment on the Chemical Fractions of Cd and As in Paddy Soil and Their Accumulation in Rice].

A pot experiment was conducted to identify the effect of a tribasic amendment (limestone+diatomite+ferric sulfate, LDF) on chemical fractions of Cd and As in paddy soils and their accumulation in brown rice. LDF was set to seven levels (0, 0.5, 1.0, 2.0, 4.0, 8.0, and 16.0 g·kg-1) based on the quality ratio, and two genotypes of rice were planted (Huanghuazhan and T-you 272). The results show that:① The application of LDF increased the rhizosphere soil pH of two varieties of rice, Huanghuazhan and T-you 272, by 0.01-0.42 and 0.11-0.54, respectively, and decreased the concentrations of EX-Cd by 11.1%-61.1% and 26.5%-52.9%, respectively, and the concentrations of EX-As by 8.2%-60.0% and 5.6%-49.9%, respectively. ② Application of LDF promoted the transformation of soil Cd and As from soluble to insoluble forms. Although the trends of the rhizosphere soils of the two rice varieties were not consistent, the application of LDF could decrease the proportion of EX-Cd and increase the proportion of Fe/Mn-Cd, Org-Cd, and O-Cd, which was accompanied by the reduction of the proportion of EX-As and an increase in the proportion of Ca-As. ③ The concentrations of Cd, As, and Fe in the iron plaque decreased by applying LDF, while the concentration of Mn increased, and the maximum increase of Mn could reach 124.2%. ④ Application of LDF decreased the concentrations of Cd in brown rice of the two varieties of rice by 64.6% and 65.9%, respectively, and decreased that of As by 37.0% and 42.5%, respectively. The effect on the concentrations of inorganic As was not significant. When the application amount of LDF was 2-16 g·kg-1, the concentrations of Cd and inorganic As in T-you 272 brown rice were both under 0.2 mg·kg-1, and when the application amount was 16 g·kg-1, the concentrations of Cd and inorganic As in Huanghuazhan brown rice were both under 0.2 mg·kg-1. In actual agricultural production, the application amount of LDF can be adjusted according to the soil pollution levels and the rice varieties.