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Biology subjects

Shevchenko, O.

Publications and source records attributed to Shevchenko, O..

2 recordsLinked to original sources

Comparative analysis of neural decoding algorithms for brain-machine interfaces

Accurate neural decoding of brain dynamics remains a significant and open challenge in brain-machine interfaces. While various signal processing, feature extraction, and classification algorithms have been proposed, a systematic comparison of these is lacking. Accordingly, here we conducted one of the largest comparative studies evaluating different combinations of state-of-the-art algorithms for motor neural decoding to find the optimal combination. We studied three signal processing methods (i.e., artifact subspace reconstruction, surface Laplacian filtering, and data normalization), four feature extractors (i.e., common spatial patterns, independent component analysis, short-time Fourier transform, and no feature extraction), and four machine learning classifiers (i.e., support vector machine, linear discriminant analysis, convolutional neural networks, and long short-term memory networks). Using a large-scale EEG dataset, we optimized each combination for individual subjects (i.e., resulting in 672 total experiments) and evaluated performance based on classification accuracy. We also compared the computational and memory storage requirements, which are important for real-time embedded computing. Our comparative analysis provides novel insights that help inform the design of next-generation neural decoding algorithms for brain-machine interfaces used to interact with and control robots and computers.

neuroscience↗

Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)

Understanding hibernation in brown bears (Ursus arctos) can provide insight into many human diseases. During hibernation, brown bears experience states of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic human diseases such as type 2 diabetes, muscle atrophy, renal and heart failure, cachexia, and obesity. The reversibility of these states from hibernation to active season allows for the identification of novel mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, we performed full-length RNA-sequencing (Iso-Seq) on three tissue types from three individuals sampled during both active and hibernation seasons. We combined the long-read data with the reference annotation for an improved transcriptome and mapped RNA-seq data from six individuals to the improved transcriptome to quantify differential isoform usage between tissues and seasons. We identified differentially expressed isoforms in all study tissues and showed that adipose has a high level of differential isoform usage with isoform switching, regardless of whether the genes were differentially expressed. Our analyses provide a comprehensive evaluation of isoform usage between active and hibernation states, revealing that differential isoform usage, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.

genomics↗