Machine Learning Methods for the Analysis of the Patch-Clamp Signals.

Patch-clamp technique provides a unique possibility to record the ion channels' activity. This method enables tracking the changes in their functional states at controlled conditions on a real-time scale. Kinetic parameters evaluated for the patch-clamp signals form the fundamentals of electrophysiological characteristics of the channel functioning. Nevertheless, the noisy series of ionic currents flowing through the channel protein(s) seem to be bountiful of information, and the standard data processing techniques likely unravel only its part. Rapid development of artificial intelligence (AI) techniques, especially machine learning (ML), gives new prospects for whole channelology. Here we consider the question of the AI applications in the patch-clamp signal analysis. It turns out that the AI methods may not only enable for automatizing of signal analysis, but also they can be used in finding inherent patterns of channel gating and allow the researchers to uncover the details of gating machinery, which had been never considered before. In this work, we outline the currently known AI methods that turned out to be utilizable and useful in the analysis of patch-clamp signals. This chapter can be considered an introductory guide to the application of AI methods in the analysis of the time series of channel currents (together with its advantages, disadvantages, and limitations), but we also propose new possible directions in this field.

Learning by confusion approach to identification of discontinuous phase transitions.

Recently, the learning by confusion (LbC) approach has been proposed as a machine learning tool to determine the critical temperature T_{c} of phase transitions without any prior knowledge of its even approximate value. The method has been proven effective, but it has been used only for continuous phase transitions, where the confusion results only from deliberate incorrect labeling of the data. However, in the case of a discontinuous phase transition, additional confusion can result from the coexistence of different phases. To verify whether the confusion scheme can also be used for discontinuous phase transitions, we apply the LbC method to three microscopic models, the Blume-Capel, the q-state Potts, and the Falicov-Kimball models, which undergo continuous or discontinuous phase transitions depending on model parameters. With the help of a simple model, we predict that the phase coexistence present in discontinuous phase transitions can indeed make the neural network more confused and thus decrease its performance. However, numerical calculations performed for the models mentioned above indicate that other aspects of this kind of phase transition are more important and can render the LbC method even less effective. Nevertheless, we demonstrate that in some cases the same aspects allow us to use the LbC method to identify the order of a phase transition.

Potassium Channels, Glucose Metabolism and Glycosylation in Cancer Cells.

Potassium channels emerge as one of the crucial groups of proteins that shape the biology of cancer cells. Their involvement in processes like cell growth, migration, or electric signaling, seems obvious. However, the relationship between the function of K+ channels, glucose metabolism, and cancer glycome appears much more intriguing. Among the typical hallmarks of cancer, one can mention the switch to aerobic glycolysis as the most favorable mechanism for glucose metabolism and glycome alterations. This review outlines the interconnections between the expression and activity of potassium channels, carbohydrate metabolism, and altered glycosylation in cancer cells, which have not been broadly discussed in the literature hitherto. Moreover, we propose the potential mediators for the described relations (e.g., enzymes, microRNAs) and the novel promising directions (e.g., glycans-orinented drugs) for further research.

Non-Monotonic Complexity of Stochastic Model of the Channel Gating Dynamics.

The simple model of an ionic current flowing through a single channel in a biological membrane is used to depict the complexity of the corresponding empirical data underlying different internal constraints and thermal fluctuations. The residence times of the channel in the open and closed states are drawn from the exponential distributions to mimic the characteristics of the real channel system. In the selected state, the dynamics are modeled by the overdamped Brownian particle moving in the quadratic potential. The simulated data allow us to directly track the effects of temperature (signal-to-noise ratio) and the channel's energetic landscape for conformational changes on the ionic currents' complexity, which are hardly controllable in the experimental case. To accurately describe the randomness, we employed four quantifiers, i.e., Shannon, spectral, sample, and slope entropies. We have found that the Shannon entropy predicts the anticipated reaction to the imposed modification of randomness by raising the temperature (an increase of entropy) or strengthening the localization (reduction of entropy). Other complexity quantifiers behave unpredictably, sometimes resulting in non-monotonic behaviour. Thus, their applicability in the analysis of the experimental time series of single-channel currents can be limited.

Flavonoids as Modulators of Potassium Channels.

Potassium channels are widely distributed integral proteins responsible for the effective and selective transport of K+ ions through the biological membranes. According to the existing structural and mechanistic differences, they are divided into several groups. All of them are considered important molecular drug targets due to their physiological roles, including the regulation of membrane potential or cell signaling. One of the recent trends in molecular pharmacology is the evaluation of the therapeutic potential of natural compounds and their derivatives, which can exhibit high specificity and effectiveness. Among the pharmaceuticals of plant origin, which are potassium channel modulators, flavonoids appear as a powerful group of biologically active substances. It is caused by their well-documented anti-oxidative, anti-inflammatory, anti-mutagenic, anti-carcinogenic, and antidiabetic effects on human health. Here, we focus on presenting the current state of knowledge about the possibilities of modulation of particular types of potassium channels by different flavonoids. Additionally, the biological meaning of the flavonoid-mediated changes in the activity of K+ channels will be outlined. Finally, novel promising directions for further research in this area will be proposed.

A New Method of Identifying Characteristic Points in the Impedance Cardiography Signal Based on Empirical Mode Decomposition.

The accurate detection of fiducial points in the impedance cardiography signal (ICG) has a decisive impact on the proper estimation of diagnostic parameters such as stroke volume or cardiac output. It is, therefore, necessary to find an algorithm that is able to assess their positions with great precision. The solution to this problem is, however, quite challenging with regard to the high sensitivity of the ICG technique to the noise and varying morphology of the acquired signals. The aim of this study is to propose a novel method that allows us to overcome these limitations. The developed algorithm is based on Empirical Mode Decomposition (EMD)-an effective technique for processing and analyzing various types of non-stationary signals. We find high correlations between the results obtained from the algorithm and annotated by an expert. This, in turn, implies that the difference in estimation of the diagnostic-relevant parameters is small, which suggests that the method can automatically provide precise clinical information.

An Effective Method of Detecting Characteristic Points of Impedance Cardiogram Verified in the Clinical Pilot Study.

Accurate and reliable determination of the characteristic points of the impedance cardiogram (ICG) is an important research problem with a growing range of applications in the cardiological diagnostics of patients with heart failure (HF). The shapes of the characteristic waves of the ICG signal and the temporal location of the characteristic points B, C, and X provide significant diagnostic information. On this basis, essential diagnostic cardiological parameters can be determined, such as, e.g., cardiac output (CO) or stroke volume (SV). Although the importance of this problem is obvious, we face many challenges, including noisy signals and the big variability in the morphology, which altogether make the accurate identification of the characteristic points quite difficult. The paper presents an effective method of ICG points identification intended for conducting experimental research in the field of impedance cardiography. Its effectiveness is confirmed in clinical pilot studies.

To what extent naringenin binding and membrane depolarization shape mitoBK channel gating-A machine learning approach.

The large conductance voltage- and Ca2+-activated K+ channels from the inner mitochondrial membrane (mitoBK) are modulated by a number of factors. Among them flavanones, including naringenin (Nar), arise as a promising group of mitoBK channel regulators from a pharmacological point of view. It is well known that in the presence of Nar the open state probability (pop) of mitoBK channels significantly increases. Nevertheless, the molecular mechanism of the mitoBK-Nar interactions remains still unrevealed. It is also not known whether the effects of naringenin administration on conformational dynamics can resemble those which are exerted by the other channel-activating stimuli. In aim to answer this question, we examine whether the dwell-time series of mitoBK channels which were obtained at different voltages and Nar concentrations (yet allowing to reach comparable pops) are discernible by means of artificial intelligence methods, including k-NN and shapelet learning. The obtained results suggest that the structural complexity of the gating dynamics is shaped both by the interaction of channel gate with the voltage sensor (VSD) and the Nar-binding site. For a majority of data one can observe stimulus-specific patterns of channel gating. Shapelet algorithm allows to obtain better prediction accuracy in most cases. Probably, because it takes into account the complexity of local features of a given signal. About 30% of the analyzed time series do not sufficiently differ to unambiguously distinguish them from each other, which can be interpreted in terms of the existence of the common features of mitoBK channel gating regardless of the type of activating stimulus. There exist long-range mutual interactions between VSD and the Nar-coordination site that are responsible for higher levels of Nar-activation (Δpop) at deeply depolarized membranes. These intra-sensor interactions are anticipated to have an allosteric nature.

Application of Machine-Learning Methods to Recognize mitoBK Channels from Different Cell Types Based on the Experimental Patch-Clamp Results.

(1) Background: In this work, we focus on the activity of large-conductance voltage- and Ca2+-activated potassium channels (BK) from the inner mitochondrial membrane (mitoBK). The characteristic electrophysiological features of the mitoBK channels are relatively high single-channel conductance (ca. 300 pS) and types of activating and deactivating stimuli. Nevertheless, depending on the isoformal composition of mitoBK channels in a given membrane patch and the type of auxiliary regulatory subunits (which can be co-assembled to the mitoBK channel protein) the characteristics of conformational dynamics of the channel protein can be altered. Consequently, the individual features of experimental series describing single-channel activity obtained by patch-clamp method can also vary. (2) Methods: Artificial intelligence approaches (deep learning) were used to classify the patch-clamp outputs of mitoBK activity from different cell types. (3) Results: Application of the K-nearest neighbors algorithm (KNN) and the autoencoder neural network allowed to perform the classification of the electrophysiological signals with a very good accuracy, which indicates that the conformational dynamics of the analyzed mitoBK channels from different cell types significantly differs. (4) Conclusion: We displayed the utility of machine-learning methodology in the research of ion channel gating, even in cases when the behavior of very similar microbiosystems is analyzed. A short excerpt from the patch-clamp recording can serve as a "fingerprint" used to recognize the mitoBK gating dynamics in the patches of membrane from different cell types.