Biology subjects

Makarova, A. V.

Publications and source records attributed to Makarova, A. V..

6 recordsLinked to original sources

bioRxiv2026

Cross-Recording Handwritten Digit Decoding from sEMG Using a Compact CNN-Transformer and Few-Shot Adaptation

Surface electromyography (sEMG) offers a silent and wearable input modality, but its practical use is limited by variability across users and recording sessions. This study presents a compact CNN- Transformer model for decoding isolated handwritten digits from eight-channel sEMG signals. The model combines trainable signal preprocessing, convolutional feature extraction, and Transformerbased temporal modeling. It was evaluated on ten recordings from five participants using recordingseen classification, leave-one-recording-out (LORO) generalization, and few-shot adaptation. The model achieved a mean macro F1 score of 0.924 {+/-} 0.059 in the recording-seen setting and 0.619 {+/-} 0.252 under zero-shot LORO evaluation. Adaptation using two labeled trials per digit increased macro F1 to 0.828 {+/-} 0.112, while ten trials per digit achieved 0.925 {+/-} 0.053. The proposed architecture also outperformed classical and neural baselines in the controlled LORO benchmark. These results indicate that compact CNN-Transformer models, combined with lightweight target-recording calibration, provide a promising basis for adaptive sEMG-based input systems.

neuroscience↗

bioRxiv2026

Opposing regulation by Rev1 of DNA polymerase zeta activity on damaged versus undamaged DNA

The Rev1 deoxycytidyl transferase functions as a scaffold protein for DNA polymerase {zeta} (Pol {zeta})-mediated translesion synthesis (TLS). Biochemical studies with yeast enzymes indicate that Rev1 plays a dual regulatory role in TLS, stimulating Pol {zeta} activity at sites of damage but inhibiting its activity on undamaged DNA. An evolutionary conserved N-terminal alpha-helical motif (M1), located 10-20 amino acids upstream of Rev1s single BRCT domain, is required for the inhibitory activity of Rev1 on undamaged DNA. Mutations in the M1 motif result in a stimulation of Pol {zeta} replication activity on both undamaged and damaged DNA. Yeast cells carrying a REV1 mutant lacking the M1 motif, show a four-fold increase in complex mutations, without significantly affecting overall spontaneous mutation rates. A catalytically inactive mutant of Rev1 still exerts these regulatory functions. However, regulation requires that Rev1 and Pol {zeta} form a stable complex, and that this complex is coordinated by the replication clamp PCNA. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/700666v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@8ed9adorg.highwire.dtl.DTLVardef@7528a3org.highwire.dtl.DTLVardef@1bf0d92org.highwire.dtl.DTLVardef@142488_HPS_FORMAT_FIGEXP M_FIG C_FIG Rev1 stimulates lesion bypass by Pol {varsigma} but inhibits Pol {varsigma} activity on undamaged DNA

biochemistry↗

bioRxiv2025

Connecting a P300 speller to a large language model

The advent of large-language models (LLMs) offers a transformative approach for improving the performance of brain-computer interface (BCI) spellers. We propose a novel framework that leverages the contextual understanding of LLMs to compensate for imperfect BCI decoding. Using existing P300 speller data, we simulated a system where users select letters to form words, generating text with characteristic spelling errors. This output is then processed by an LLM, which corrects the errors - a task that becomes more effective when the model considers full-sentence context. Our findings suggest that this synergy can accelerate communication rates by relaxing the need for high single-character accuracy. Beyond speed, integrating an LLM transforms the BCI into an intelligent agent, capable of acting as a discussant and assistant, thereby enriching the user experience.

neuroscience↗

bioRxiv2025

Beyond Traditional Poincare Analysis: Second-Order Plots Reveal Respiratory Effects in Heart Rate Variability

Heart rate variability (HRV) is a non-invasive biomarker of autonomic nervous system activity, commonly analyzed using a Poincare plot. This plot visualizes correlations between successive heartbeats (RRi vs. RRi+1) and quantifies autonomic regulation through SD1 and SD2 parameters. We introduce a second-order Poincare plot, a natural extension that clarifies serial dependencies by plotting successive differences in RR intervals ({Delta}RRi vs. {Delta}RRi+1). Applied to a PhysioNet dataset of 20 healthy individuals, this technique filtered out the slow HRV baseline of traditional elliptical plots to reveal distinct higher-order dynamics. These included ring-shaped structures indicating cardiorespiratory synchronization. A coupled-oscillator model, developed to simulate respiratory modulation, confirmed that these patterns are dictated by the respiratory frequency to heart rate ratio: slower breathing produces positive serial correlations in {Delta}RR, while faster breathing induces negative ones. By visualizing serial dependencies that conventional HRV metrics miss, the second-order Poincare plot extends the classical analysis framework. This tool provides a refined method for uncovering subtle dynamical features in HRV across diverse physiological and clinical states. HighlightsO_LISecond-order Poincare plots, plotting successive differences of RR intervals ({Delta}RRi vs. {Delta}RRi+1), extend traditional Poincare analysis to reveal rapid HRV dynamics. C_LIO_LIIn a dataset of 20 healthy individuals, second-order plots filtered out slow HRV components, highlighting respiratory modulation. C_LIO_LIRing-shaped patterns in some participants indicated strong cardiorespiratory coupling, while others showed positive or negative serial correlations linked to breathing rate. C_LIO_LIA coupled-oscillator model confirmed that the ratio of respiratory to heart rate frequency determines serial correlation patterns. C_LIO_LIThis method offers a novel tool for analyzing HRV dynamics, with potential applications in physiological and clinical research. C_LI

physiology↗

bioRxiv2023

PrimPol variant V102A with altered primase and polymerase activities

PrimPol is a human DNA primase-polymerase which restarts DNA synthesis beyond DNA lesions and non-B DNA structures blocking replication. Disfunction of PrimPol in cells leads to slowing of DNA replication rates in mitochondria and nucleus, accumulation of chromosome aberrations, cell cycle delay, elevated sensitivity to DNA-damaging agents. PrimPol has been suggested to be associated with the development of ophthalmic diseases, elevated mitochondrial toxicity of antiviral drugs and increased cell resistance to chemotherapy. Here, we describe a rare missense PrimPol variant V102A with altered biochemical properties identified in patients suffering from ovarian and cervical cancer. The Val102Ala substitution dramatically reduced both the primase and DNA polymerase activities of PrimPol as well as specifically decreased its ability to incorporate ribonucleotides. We suggest that substitutions in this region would likely distort the active site and affect the catalytic activity of PrimPol.

biochemistry↗

bioRxiv2023

The role of catalytic and regulatory domains of human PrimPol in DNA binding and synthesis

Human PrimPol possesses DNA primase and DNA polymerase activities and restarts stalled replication forks protecting cells against DNA damage in nuclei and mitochondria. The zinc-binding motif (ZnFn) of the C-terminal domain (CTD) of PrimPol is required for DNA primase activity but the mechanism is not clear. In this work, we biochemically demonstrate that PrimPol initiates de novo DNA synthesis in cis-orientation, when the N-terminal catalytic domain (NTD) and the CTD of one molecule take part in catalysis. The modeling studies revealed that PrimPol uses a similar mode of initiating NTP coordination as the human primase. The ZnFn motif residue Arg417 is required for binding the 5-triphosphate group that stabilizes the PrimPol complex with a DNA template-primer. We found that PrimPol is able to efficiently initiate DNA synthesis in the absence of the link between the two domains. The ability of the NTD alone to prime DNA synthesis and a regulatory role of the RPA-binding motif in the modulation of PrimPol binding to DNA are also demonstrated.

biochemistry↗