DeepVariant has revolutionized the field of genetic variant identification by reframing variant detection as an image classification problem. However, despite its wide adoption in bioinformatics workflows, the tool continues to evolve mainly through the expansion of training datasets, while its core neural network architecture—Inception V3—has remained unchanged. In this study, we revisited the DeepVariant design and presented a prototype of a modernized version that supports alternative neural network backbones. As a proof of concept, we replaced the legacy Inception V3 model with a mid-sized EfficientNet model and evaluated its performance using the benchmark dataset from the Genome in a Bottle (GIAB) project. Alternative architecture demonstrated faster convergence, a twofold reduction in the number of parameters, and improved accuracy in variant identification. On the test dataset, updated workflow achieved consistent improvements of +0.1% in SNP F1-score, enabling the detection of up to several hundred additional true variants per genome. These results show that optimizing the neural architecture alone can enhance the accuracy, robustness, and efficiency of variant calling, thereby improving the overall quality of sequencing data analysis.

Neurodegenerative diseases pose a significant challenge to modern medicine. Despite significant advances in neurology, current therapeutic approaches often prove insufficient to treat such disorders. This study investigates the neuroprotective effect of extracellular vesicles derived from glial derivates of human-induced pluripotent stem cells. The extracellular vesicle’s cargo was characterised by proteomic analysis. The neuroprotective effect was assessed using a model of glutamate excitotoxicity performed on a primary culture of cortical neuroglial cells. The viability of cells was estimated using the MTT test and morphometric analyses. A comprehensive methodology was applied to investigate intracellular mechanisms, integrating assessments of intracellular calcium concentrations, mitochondrial membrane potential, and targeted inhibition of the PI3K-Akt pathway. Transcriptomic analysis of neuroglial cultures was used to validate the role of obtained mechanisms of extracellular vesicle’s neuroprotective effect. The obtaining results demonstrated the improvement of neuronal survival by reducing intracellular calcium levels and stabilising mitochondrial membrane potential under glutamate-induced excitotoxicity via PI3K-Akt signalling pathway activation. Moreover, the vesicles contained proteins that contribute to preventing apoptotic processes, activating regeneration of the nervous system, and modulating calcium ion transport and are associated with redox processes. Further transcriptomic analyses of neuroglial cultures treated with EVs showed an up-regulation of genes associated with regeneration, inhibition of calcium ion transport, regulation of membrane depolarisation, and negative regulation of apoptotic pathways.

Neurodegenerative diseases pose a significant challenge to modern medicine. Despite significant advances in neurology, current therapeutic approaches often prove insufficient to treat such disorders. This study investigates the neuroprotective effect of extracellular vesicles derived from glial derivates of human induced pluripotent stem cells. The extra-cellular vesicle’s cargo was characterised by proteomic analysis. They neuroprotective ef-fect was assessed using a model of glutamate excitotoxicity performed on primary culture of cortical neurons. The viability of cortical neurons was estimated using the MTT test and morphometric analyses. A comprehensive methodology was applied to investigate intra-cellular mechanisms, integrating assessments of intracellular calcium concentrations, mitochondrial membrane potential, and targeted inhibition of the PI3K‑Akt pathway. Transcriptomic analysis of cortical neurons was used to validated the role of obtained mechanisms of extracellular vesicle’s neuroprotective effect. The obtaining results demon-strated the improvement of neuronal survival by reducing intracellular calcium levels, and stabilizing mitochondrial membrane potential under glutamate-induced excitotoxi-city via PI3K-Akt signaling pathway activation. Moreover, the vesicles contained proteins that contribute to preventing apoptotic processes, activating regeneration of nervous sys-tem, modulating of calcium ion transport and associated with redox processes. Further transcriptomic analyses of neuroglial cultures treated with EVs showed up-regulation of genes associated with regeneration, inhibition of calcium ion transport, regulation of membrane depolirisation and negative regulation of apoptotic pathways.