Biology subjects

Smetanin, N.

Publications and source records attributed to Smetanin, N..

5 recordsLinked to original sources

bioRxiv2022

A high-level programming language for generative protein design

Combining a basic set of building blocks into more complex forms is a universal design principle. Most protein designs have proceeded from a manual bottom-up approach using parts created by nature, but top-down design of proteins is fundamentally hard due to biological complexity. We demonstrate how the modularity and programmability long sought for protein design can be realized through generative artificial intelligence. Advanced protein language models demonstrate emergent learning of atomic resolution structure and protein design principles. We leverage these developments to enable the programmable design of de novo protein sequences and structures of high complexity. First, we describe a high-level programming language based on modular building blocks that allows a designer to easily compose a set of desired properties. We then develop an energy-based generative model, built on atomic resolution structure prediction with a language model, that realizes all-atom structure designs that have the programmed properties. Designing a diverse set of specifications, including constraints on atomic coordinates, secondary structure, symmetry, and multimerization, demonstrates the generality and controllability of the approach. Enumerating constraints at increasing levels of hierarchical complexity shows that the approach can access a combinatorially large design space.

synthetic biology↗

bioRxiv2021

Cortical and autonomic responses during staged Taoist meditation: two distinct meditation strategies.

Meditation is a consciousness state associated with specific physiological and neural correlates. Numerous investigations of these correlates reported controversial results which prevented a consistent depiction of the underlying neurophysiological processes. Here we investigated the dynamics of multiple neurophysiological indicators during a staged meditation session. We measured the physiological changes at rest and during the guided Taoist meditation in experienced meditators and naive subjects. We recorded EEG, respiration, galvanic skin response, and photoplethysmography. All subjects followed the same instructions split into 16 stages. In the experienced meditators group we identified two subgroups with different physiological markers dynamics. One subgroup showed several signs of general relaxation evident from the changes in heart rate variability, respiratory rate, and EEG rhythmic activity. The other subgroup exhibited mind concentration patterns primarily noticeable in the EEG recordings while no autonomic responses occurred. The duration and type of previous meditation experience or any baseline indicators we measured did not explain the segregation of the meditators into these two groups. These results suggest that two distinct meditation strategies could be used by experienced meditators, which partly explains the inconsistent results reported in the earlier studies evaluating meditation effects. Our findings are also relevant to the development of the high-end biofeedback systems.

physiology↗

bioRxiv2020

The importance of being on time: delayed neurofeedback impedes training of the parietal alpha-band power

The therapeutic effects of neurofeedback (NFB) remain controversial. Here we show that visual NFB of parietal electroencephalographic (EEG) alpha-activity is efficient only when delivered to human subjects at short latency, which guarantees that NFB arrives when an alpha spindle is still ongoing. NFB was displayed either as soon as EEG envelope was processed, or with an extra 250 or 500-ms delay. The time course of NFB-induced changes in the alpha rhythm clearly depended on NFB latency, as shown with the adaptive Neyman test. NFB had a strong effect on the alpha-spindle incidence rate, but not on their duration or amplitude. The sustained changes in alpha activity measured after the completion of NFB training were negatively correlated to latency, with the maximum change for the shortest tested latency and no change for the longest. Such a considerable effect of NFB latency on the alpha-activity temporal structure could explain some of the previous inconsistent results, where latency was neither controlled nor documented. Clinical practitioners and manufacturers of NFB equipment should add latency to their specifications while enabling latency monitoring and supporting short-latency operations.

neuroscience↗

bioRxiv2019

Closed-loop Neuroscience of brain rhythms: optimizing real-time quantification of narrow-band signals to expedite feedback delivery

AO_SCPLOWBSTRACTC_SCPLOWClosed-loop Neuroscience is based on the experimental approach where the ongoing brain activity is recorded, processed, and passed back to the brain as sensory feedback or direct stimulation of neural circuits. The artificial closed loops constructed with this approach expand the traditional stimulus-response experimentation. As such, closed-loop Neuroscience provides insights on the function of loops existing in the brain and the ways the flow of neural information could be modified to treat neurological conditions. Neural oscillations, or brain rhythms, are a class of neural activities that have been extensively studied and also utilized in brain rhythm-contingent (BRC) paradigms that incorporate closed loops. In these implementations, instantaneous power and phase of neural oscillations form the signal that is fed back to the brain. Here we addressed the problem of feedback delay in BRC paradigms. In many BRC systems, it is critical to keep the delay short. Long delays could render the intended modification of neural activity impossible because the stimulus is delivered after the targeted neural pattern has already completed. Yet, the processing time needed to extract oscillatory components from the broad-band neural signals can significantly exceed the period of oscillations, which puts a demand for algorithms that could minimize the delay. We used EEG data collected in human subjects to systematically investigate the performance of a range of signal processing methods in the context of minimizing delay in BRC systems. We proposed a family of techniques based on the least-squares filter design - a transparent and simple approach, as it required a single parameter to adjust the accuracy versus latency trade-off. Our algorithm performed on par or better than the state-of the art techniques currently used for the estimation of rhythm envelope and phase in closed-loop EEG paradigms.

neuroscience↗

bioRxiv2018

Towards zero-latency neurofeedback

Neurofeedback (NFB) is a real-time paradigm, where subjects monitor their own brain activity presented to them via one of the sensory modalities: visual, auditory or tactile. NFB has been proposed as an approach to treat neurological conditions and augment brain functions. In many applications, especially in the automatic learning scenario it is important to decrease NFB latency, so that appropriate brain mechanisms can be efficiently engaged. To this end, we propose a novel algorithm that significantly reduces feedback signal presentation in the electroencephalographic (EEG) NFB paradigm. The algorithm is based on the least squares optimization of the finite impulse response (FIR) filter weights and analytic signal reconstruction. In this approach, the trade-off between NFB latency and the accuracy of EEG envelope estimation can be achieved depending on the application needs. Moreover, the algorithm allows to implement predictive NFB by setting latency to negative values while maintaining acceptable envelope estimation accuracy. As such, our algorithm offers significant improvements in cases where subjects need to detect neural events as soon as possible and even in advance.

bioinformatics↗