Signatures of chaotic and stochastic dynamics uncovered with ε -recurrence networks

An old and important problem in the field of nonlinear time-series analysis entails the distinction between chaotic and stochastic dynamics. Recently, ε -recurrence networks have been proposed as a tool to analyse the structural properties of a time series. In this paper, we propose the applicability of local and global ε -recurrence network measures to distinguish between chaotic and stochastic dynamics using paradigmatic model systems such as the Lorenz system, and the chaotic and hyper-chaotic Rössler system. We also demonstrate the effect of increasing levels of noise on these network measures and provide a real-world application of analysing electroencephalographic data comprising epileptic seizures. Our results show that both local and global ε -recurrence network measures are sensitive to the presence of unstable periodic orbits and other structural features associated with chaotic dynamics that are otherwise absent in stochastic dynamics. These network measures are still robust at high noise levels and short data lengths. Furthermore, ε -recurrence network analysis of the real-world epileptic data revealed the capability of these network measures in capturing dynamical transitions using short window sizes. ε -recurrence network analysis is a powerful method in uncovering the signatures of chaotic and stochastic dynamics based on the geometrical properties of time series.

Human induced pluripotent stem cell-derived versus adult cardiomyocytes: an in silico electrophysiological study on effects of ionic current block

Background and Purpose

Two new technologies are likely to revolutionize cardiac safety and drug development: in vitro experiments on human‐induced pluripotent stem cell‐derived cardiomyocytes (hiPSC‐CMs) and in silico human adult ventricular cardiomyocyte (hAdultV‐CM) models. Their combination was recently proposed as a potential replacement for the present hERG‐based QT study for pharmacological safety assessments. Here, we systematically compared in silico the effects of selective ionic current block on hiPSC‐CM and hAdultV‐CM action potentials (APs), to identify similarities/differences and to illustrate the potential of computational models as supportive tools for evaluating new in vitro technologies.

Experimental Approach

In silico AP models of ventricular‐like and atrial‐like hiPSC‐CMs and hAdultV‐CM were used to simulate the main effects of four degrees of block of the main cardiac transmembrane currents.

Key Results

Qualitatively, hiPSC‐CM and hAdultV‐CM APs showed similar responses to current block, consistent with results from experiments. However, quantitatively, hiPSC‐CMs were more sensitive to block of (i) L‐type Ca²⁺ currents due to the overexpression of the Na⁺/Ca²⁺ exchanger (leading to shorter APs) and (ii) the inward rectifier K⁺ current due to reduced repolarization reserve (inducing diastolic potential depolarization and repolarization failure).

Conclusions and Implications

In silico hiPSC‐CMs and hAdultV‐CMs exhibit a similar response to selective current blocks. However, overall hiPSC‐CMs show greater sensitivity to block, which may facilitate in vitro identification of drug‐induced effects. Extrapolation of drug effects from hiPSC‐CM to hAdultV‐CM and pro‐arrhythmic risk assessment can be facilitated by in silico predictions using biophysically‐based computational models.

Investigating local spatially-enhanced structural and textural descriptors for classification of iPSC colony images

Induced pluripotent stem cells (iPSC) can be derived from fully differentiated cells of adult individuals and used to obtain any other cell type of the human body. This implies numerous prospective applications of iPSCs in regenerative medicine and drug development. In order to obtain valid cell culture, a quality control process must be applied to identify and discard abnormal iPSC colonies. Computer vision systems that analyze visual characteristics of iPSC colony health can be especially useful in automating and improving the quality control process. In this paper, we present an ongoing research that aims at the development of local spatially-enhanced descriptors for classification of iPSC colony images. For this, local oriented edges and local binary patterns are extracted from the detected colony regions and used to represent structural and textural properties of the colonies, respectively. We preliminary tested the proposed descriptors in classifying iPSCs colonies according to the degree of colony abnormality. The tests showed promising results for both, detection of iPSC colony borders and colony classification.

Controlling cell migration and adhesion into a scaffold by external electric currents

Fabrication of more complex tissue-engineered structures, resembling the tissues and organs in vivo requires combining more than one cell type within the same construct. This can be achieved by designing and fabricating complex scaffolds with asymmetric properties but controlled arrangement of cells within the scaffold could also be realized by using electric current. External electric currents are able to modify cell adhesion, orientation and migration and this can be used for influencing cell location within a scaffold. In this paper we studied the effect of an electric current on cell migration and adhesion into a three-dimensional scaffold through a conductive mesh.

Computational Model of Ca2+ Wave Propagation in Human Retinal Pigment Epithelial ARPE-19 Cells

Objective

Computational models of calcium (Ca²⁺) signaling have been constructed for several cell types. There are, however, no such models for retinal pigment epithelium (RPE). Our aim was to construct a Ca²⁺ signaling model for RPE based on our experimental data of mechanically induced Ca²⁺ wave in the in vitro model of RPE, the ARPE-19 monolayer.

Methods

We combined six essential Ca²⁺ signaling components into a model: stretch-sensitive Ca²⁺ channels (SSCCs), P₂Y₂ receptors, IP₃ receptors, ryanodine receptors, Ca²⁺ pumps, and gap junctions. The cells in our epithelial model are connected to each other to enable transport of signaling molecules. Parameterization was done by tuning the above model components so that the simulated Ca²⁺ waves reproduced our control experimental data and data where gap junctions were blocked.

Results

Our model was able to explain Ca²⁺ signaling in ARPE-19 cells, and the basic mechanism was found to be as follows: 1) Cells near the stimulus site are likely to conduct Ca²⁺ through plasma membrane SSCCs and gap junctions conduct the Ca²⁺ and IP³ between cells further away. 2) Most likely the stimulated cell secretes ligand to the extracellular space where the ligand diffusion mediates the Ca²⁺ signal so that the ligand concentration decreases with distance. 3) The phosphorylation of the IP₃ receptor defines the cell’s sensitivity to the extracellular ligand attenuating the Ca²⁺ signal in the distance.

Conclusions

The developed model was able to simulate an array of experimental data including drug effects. Furthermore, our simulations predict that suramin may interfere ligand binding on P₂Y₂ receptors or accelerate P₂Y₂ receptor phosphorylation, which may partially be the reason for Ca²⁺ wave attenuation by suramin. Being the first RPE Ca²⁺ signaling model created based on experimental data on ARPE-19 cell line, the model offers a platform for further modeling of native RPE functions.

Investigating the possible effect of electrode support structure on motion artifact in wearable bioelectric signal monitoring

Background

With advances in technology and increasing demand, wearable biosignal monitoring is developing and new applications are emerging. One of the main challenges facing the widespread use of wearable monitoring systems is the motion artifact. The sources of the motion artifact lie in the skin–electrode interface. Reducing the motion and deformation at this interface should have positive effects on signal quality. In this study, we aim to investigate whether the structure supporting the electrode can be designed to reduce the motion artifact with the hypothesis that this can be achieved by stabilizing the skin deformations around the electrode.

Methods

We compare four textile electrodes with different support structure designs: a soft padding larger than the electrode area, a soft padding larger than the electrode area with a novel skin deformation restricting design, a soft padding the same size as the electrode area, and a rigid support the same size as the electrode. With five subjects and two electrode locations placed over different kinds of tissue at various mounting forces, we simultaneously measured the motion artifact, a motion affected ECG, and the real-time skin–electrode impedance during the application of controlled motion to the electrodes.

Results

The design of the electrode support structure has an effect on the generated motion artifact; good design with a skin stabilizing structure makes the electrodes physically more motion artifact resilient, directly affecting signal quality. Increasing the applied mounting force shows a positive effect up to 1,000 gr applied force. The properties of tissue under the electrode are an important factor in the generation of the motion artifact and the functioning of the electrodes. The relationship of motion artifact amplitude to the electrode movement magnitude is seen to be linear for smaller movements. For larger movements, the increase of motion generated a disproportionally larger artifact. The motion artifact and the induced impedance change were caused by the electrode motion and contained the same frequency components as the applied electrode motion pattern.

Conclusion

We found that stabilizing the skin around the electrode using an electrode structure that manages to successfully distribute the force and movement to an area beyond the borders of the electrical contact area reduces the motion artifact when compared to structures that are the same size as the electrode area.

Distinct electrophysiological and mechanical beating phenotypes of long QT syndrome type 1-specific cardiomyocytes carrying different mutations

Background

Long QT syndrome (LQTS) is associated with increased risk of ventricular arrhythmias and cardiac arrest. LQTS type 1 (LQT1), the most prevalent subtype of LQTS, is caused by defects of slow delayed rectifier potassium current (I_Ks) that lead to abnormal cardiac repolarization. Here we used pluripotent stem cell (iPSC)-technology to investigate both the electrophysiological and also for the first time the mechanical beating behavior of genetically defined, LQT1 specific cardiomyocytes (CMs) carrying different mutations.

Methods

We established in vitro models for LQT1 caused by two mutations (G589D or ivs7-2A>G). LQT1 specific CMs were derived from patient specific iPSCs and characterized for their electrophysiology using a current clamp and Ca^2 +-imaging. Their mechanical beating characteristics were analyzed with video-image analysis method.

Results and conclusions

Both LQT1-CM-types showed prolonged repolarization, but only those with G589D presented early after-depolarizations at baseline. Increased amounts of abnormal Ca^2 + transients were detected in both types of LQT1-CMs. Surprisingly, also the mechanical beating behavior demonstrated clear abnormalities and additionally the abnormalities were different with the two mutations: prolonged contraction was seen in G589D-CMs while impaired relaxation was observed in ivs7-2A>G-CMs.

The CMs carrying two different LQT1 specific mutations (G589D or ivs7-2A>G) presented clear differences in their electrical properties as well as in their mechanical beating behavior. Results from different methods correlated well with each other suggesting that simply mechanical beating behavior of CMs could be used for screening of diseased CMs and possibly for diagnostic purposes in the future.

Dynamics of intracranial electroencephalographic recordings from epilepsy patients using univariate and bivariate recurrence networks

Recently Andrezejak et al. combined the randomness and nonlinear independence test with iterative amplitude adjusted Fourier transform (iAAFT) surrogates to distinguish between the dynamics of seizure-free intracranial electroencephalographic (EEG) signals recorded from epileptogenic (focal) and nonepileptogenic (nonfocal) brain areas of epileptic patients. However, stationarity is a part of the null hypothesis for iAAFT surrogates and thus nonstationarity can violate the null hypothesis. In this work we first propose the application of the randomness and nonlinear independence test based on recurrence network measures to distinguish between the dynamics of focal and nonfocal EEG signals. Furthermore, we combine these tests with both iAAFT and truncated Fourier transform (TFT) surrogate methods, which also preserves the nonstationarity of the original data in the surrogates along with its linear structure. Our results indicate that focal EEG signals exhibit an increased degree of structural complexity and interdependency compared to nonfocal EEG signals. In general, we find higher rejections for randomness and nonlinear independence tests for focal EEG signals compared to nonfocal EEG signals. In particular, the univariate recurrence network measures, the average clustering coefficient C and assortativity R, and the bivariate recurrence network measure, the average cross-clustering coefficient C(cross), can successfully distinguish between the focal and nonfocal EEG signals, even when the analysis is restricted to nonstationary signals, irrespective of the type of surrogates used. On the other hand, we find that the univariate recurrence network measures, the average path length L, and the average betweenness centrality BC fail to distinguish between the focal and nonfocal EEG signals when iAAFT surrogates are used. However, these two measures can distinguish between focal and nonfocal EEG signals when TFT surrogates are used for nonstationary signals. We also report an improvement in the performance of nonlinear prediction error N and nonlinear interdependence measure L used by Andrezejak et al., when TFT surrogates are used for nonstationary EEG signals. We also find that the outcome of the nonlinear independence test based on the average cross-clustering coefficient C(cross) is independent of the outcome of the randomness test based on the average clustering coefficient C. Thus, the univariate and bivariate recurrence network measures provide independent information regarding the dynamics of the focal and nonfocal EEG signals. In conclusion, recurrence network analysis combined with nonstationary surrogates can be applied to derive reliable biomarkers to distinguish between epileptogenic and nonepileptogenic brain areas using EEG signals.

Micro CT visualization of silver nanoparticles in the middle and inner ear of rat and transportation pathway after transtympanic injection

Background

Silver nanoparticles (Ag NPs) displayed strong activities in anti-bacterial, anti-viral, and anti-fungal studies and were reportedly efficient in treating otitis media. Information on distribution of AgNPs in different compartments of the ear is lacking.

Objective

To detect distribution of Ag NPs in the middle and inner ear and transportation pathways after transtympanic injection.

Methods

Contrast effect of Ag NPs in the micro CT imaging was assessed in a phantom. AgNPs at various concentrations (1.85 mM, 37.1 mM, and 370.7 mM) were administered to rat middle ear using transtympanic injection and cadaver heads were imaged using micro CT at several time points.

Results

The lowest concentration of Ag NPs that could be visualized using micro CT was 37.1 mM. No difference was observed between the solvents, deionized H₂O and saline. Ag NPs at 37.1 mM were visible in the middle ear on 7 d post-administration. Ag NPs at 370.7 mM generated signals in the middle ear, ossicular chain, round window membrane, oval window, scala tympani, and Eustachian tube for both 4 h and 24 h time points. A gradient distribution of Ag NPs from the middle ear to the inner ear was detected. The pathways for Ag NPs to be transported from the middle ear into the inner ear are round and oval windows.

Conclusion

This study provided the imaging evidence that Ag NPs are able to access the inner ear in a dose-dependent manner after intratympanic administration, which is relevant to design the delivery concentration in the future clinic application in order to avoid adverse inner ear effect.

A multi-tissue segmentation of the human head for detailed computational models

This paper describes the creation of an anatomically detailed high resolution model of the human head based on the Visible Human Female data from the National Library of Medicine archives. Automatic and semi-automatic segmentation algorithms were applied over the 3 image volumes – CT, MRI and anatomical cryo-sections of the cadaver – to label a total of 23 tissues. The results were combined to create a labeled volume of the head with voxel dimensions of 0.33×0.33×0.33 mm. The individual label matrices and their corresponding surface meshes are made available to be used freely. The detailed blood vessel network and ocular tissues will be of interest in computational modelling and simulation studies.

Recurrence network analysis of multiple local field potential bands from the orofacial portion of primary motor cortex

Local field potentials (LFPs), which have been considered as aggregate signals that reflect activities of a large number of neurons in the cerebral cortex, have been observed to mediate gross functional activities of a relatively small volume of the brain tissues. Historically there have been several frequency bands observed and defined across various brain areas. However, detailed analysis, either spectral analysis or any dynamical analysis of LFPs particularly in the orofacial part of the primary motor cortex (MIo) has not been done before. Here, we recorded LFPs from MIo using an electrode array from a non-human primate during feeding behavior. Then we performed spectral analysis during the whole feeding sequences and to characterize temporal evolution of spectrum around the time of swallow cycles. The spectrogram over the β range showed dynamical change in its power around the swallow cycle onsets. We then characterized dynamical behaviors of LFPs over multiple bands, α, β, low γ, and high γ using two measures from the recurrence network (RN) method, network transitivity, T and average path length L. Temporal profile of T in α and β indicated that there was a sudden change in the dynamical properties around the swallow cycle onsets, while temporal profile of L indicated that a range of -200 to -150 ms and 200 ms to the swallow cycle onsets exhibited large changes both in α and β ranges. Therefore, to further understand the involvement of cortical oscillation to behavior, particularly swallowing, the combination of traditional spectral methods and various dynamical methods such as RN method would be essential.

A motion artifact generation and assessment system for the rapid testing of surface biopotential electrodes

Dry electrodes can reduce cost while increasing the usability and comfort of wearable monitoring systems. They are, however, susceptible to motion artifacts. The present electrode testing methods lack reliability and do not separate the factors that affect the motion artifact. In this paper, we introduce a first generation motion artifact generation and assessment system that generates the speed, amplitude, and pattern-wise programmable movement of the electrode. The system simultaneously measures electrode-skin impedance, the motion artifact, and one channel of an electrocardiogram that contains the motion artifact and monitors the mounting force applied to the electrode. We demonstrate the system by comparing the applied movement and the measured signals for electrode movements up to 6 mm and movement frequencies from 0.4 Hz to 4 Hz. Results show that the impedance change and surface potential are visually clearly related to the applied motion, with average correlations of 0.89 and 0.64, respectively. The applied force, electrode location, and electrode structure all affect the motion artifact. The setup enables the motion of the electrode to be accurately controlled. The system can be used as a precursor to the testing of integrated systems because it enables thorough, repeatable, and robust motion artifact studies. The system allows a deeper insight into motion artifacts and the interplay of the various factors that affect them.

Impedance spectroscopy of changes in skin-electrode impedance induced by motion

BACKGROUND

The motion artifact is an ever-present challenge in the mobile monitoring of surface potentials. Skin-electrode impedance is investigated as an input parameter to detect the motion artifact and to reduce it using various methods. However, the impact of the used impedance measurement frequency on the relationship between measured impedance and the motion artifact and the relationship between the impedance and the motion is not well understood.

METHODS

In this paper, for the first time, we present the simultaneous measurement of impedance at 8 current frequencies during the application of controlled motion to the electrode at monitored electrode mounting force. Three interwoven frequency groupings are used to obtain a spectrum of 24 frequencies between 25 Hz and 1 MHz for ten volunteers. Consequently, the surface potential and one channel of ECG are measured from the electrode subject to controlled motion. The signals are then analyzed in time and frequency domain.

RESULTS

The results show that the different frequencies of impedance measurements do not reflect the motion in the same manner. The best correlation between impedance and the applied motion was seen at impedance current frequencies above 17 kHz. For resistance this relationship existed for frequencies above 11 kHz, Reactance did not show good time domain correlation, but had good frequency domain correlation at frequencies higher than 42 kHz. Overall, we found that the impedance signal correlated well with the applied motion; however impedance had lower correlation to actual motion artifact signal.

CONCLUSION

Based on our results, we can conclude that the current frequency used for the impedance measurement has a great effect on the relationship of the measurement to the applied motion and its relationship with the resulting motion artifact. Therefore, when flat textile contact biopotential electrodes are used, frequencies higher than 17 kHz are best suited for impedance measurements intended for the estimation of electrode motion or motion artifact. For resistance, the best frequencies to use are higher than 11 kHz.

Optical projection tomography as a tool for 3D imaging of hydrogels

An Optical Projection Tomography (OPT) system was developed and optimized to image 3D tissue engineered products based in hydrogels. We develop pre-reconstruction algorithms to get the best result from the reconstruction procedure, which include correction of the illumination and determination of sample center of rotation (CoR). Existing methods for CoR determination based on the detection of the maximum variance of reconstructed slices failed, so we develop a new CoR search method based in the detection of the variance sharpest local maximum. We show the capabilities of the system to give quantitative information of different types of hydrogels that may be useful in its characterization.

Characterization of microstructures using contour tree connectivity for fluid flow analysis

Quantifying the connectivity of material microstructures is important for a wide range of applications from filters to biomaterials. Currently, the most used measure of connectivity is the Euler number, which is a topological invariant. Topology alone, however, is not sufficient for most practical purposes. In this study, we use our recently introduced connectivity measure, called the contour tree connectivity (CTC), to study microstructures for flow analysis. CTC is a new structural connectivity measure that is based on contour trees and algebraic graph theory. To test CTC, we generated a dataset composed of 120 samples and six different types of artificial microstructures. We compared CTC against the Euler parameter (EP), the parameter for connected pairs, the nominal opening dimension (dnom) and the permeabilities estimated using direct pore scale modelling. The results show that dnom is highly correlated with permeability (R2=0.91), but cannot separate the structural differences. The groups are best classified with feature combinations that include CTC. CTC provides new information with a different connectivity interpretation that can be used to analyse and design materials with complex microstructures.

Bone loss patterns in cortical, subcortical, and trabecular compartments during simulated microgravity

Disuse studies provide a useful model for bone adaptation. A direct comparison of these studies is, however, complicated by the different settings used for bone analysis. Through pooling and reanalysis of bone data from previous disuse studies, we determined bone loss and recovery in cortical, subcortical, and trabecular compartments and evaluated whether the study design modulated skeletal adaptation. Peripheral quantitative tomographic (pQCT) images from control groups of four disuse studies with a duration of 24, 35, 56, and 90 days were reanalyzed using a robust threshold-free segmentation algorithm. The pQCT data were available from 27 young healthy men at baseline, and at specified intervals over disuse and reambulation phases. The mean maximum absolute bone loss (mean ± 95% CI) was 6.1 ± 4.5 mg/mm in cortical, 2.4 ± 1.6 mg/mm in subcortical, and 9.8 ± 9.1 mg/mm in trabecular compartments, after 90 days of bed rest. The percentage changes in all bone compartments were, however, similar. During the first few weeks after onset of reambulation, the bone loss rate was systematically greater in the cortical than in the trabecular compartment (P < 0.002), and this was observed in all studies except for the longest study. We conclude that disuse-induced bone losses follow similar patterns irrespective of study design, and the largest mean absolute bone loss occurs in the cortical compartment, but apparently only during the first 60 days. With longer study duration, trabecular loss may become more prominent.

Video image-based analysis of single human induced pluripotent stem cell derived cardiomyocyte beating dynamics using digital image correlation

Background

The functionality of a cardiomyocyte is primarily measured by analyzing the electrophysiological properties of the cell. The analysis of the beating behavior of single cardiomyocytes, especially ones derived from stem cells, is challenging but well warranted. In this study, a video-based method that is non-invasive and label-free is introduced and applied for the study of single human cardiomyocytes derived from induced pluripotent stem cells.

Methods

The beating of dissociated stem cell-derived cardiomyocytes was visualized with a microscope and the motion was video-recorded. Minimum quadratic difference, a digital image correlation method, was used for beating analysis with geometrical sectorial cell division and radial/tangential directions. The time series of the temporal displacement vector fields of a single cardiomyocyte was computed from video data. The vector field data was processed to obtain cell-specific, contraction-relaxation dynamics signals. Simulated cardiomyocyte beating was used as a reference and the current clamp of real cardiomyocytes was used to analyze the electrical functionality of the beating cardiomyocytes.

Results

Our results demonstrate that our sectorized image correlation method is capable of extracting single cell beating characteristics from the video data of induced pluripotent stem cell-derived cardiomyocytes that have no clear movement axis, and that the method can accurately identify beating phases and time parameters.

Conclusion

Our video analysis of the beating motion of single human cardiomyocytes provides a robust, non-invasive and label-free method to analyze the mechanobiological functionality of cardiomyocytes derived from induced pluripotent stem cells. Thus, our method has potential for the high-throughput analysis of cardiomyocyte functions.

Analysis of virus textures in transmission electron microscopy images

In this paper we propose an ensemble of texture descriptors for analyzing virus textures in transmission electron microscopy images. Specifically, we present several novel multi-quinary (MQ) codings of local binary pattern (LBP) variants: the MQ version of the dense LBP, the MQ version of the rotation invariant co-occurrence among adjacent LBPs, and the MQ version of the LBP histogram Fourier. To reduce computation time as well as to improve performance, a feature selection approach is utilized to select the thresholds used in the MQ approaches. In addition, we propose new variants of descriptors where two histograms, instead of the standard one histogram, are produced for each descriptor. The two histograms (one for edge pixels and the other for non-edge pixels) are calculated for training two different SVMs, whose results are then combined by sum rule. We show that a bag of features approach works well with this problem. Our experiments, using a publicly available dataset of 1500 images with 15 classes and same protocol as in previous works, demonstrate the superiority of our new proposed ensemble of texture descriptors. The MATLAB code of our approach is available at https://www.dei.unipd.it/node/2357.

Novel electrode configuration for highly linear impedance pneumography

Impedance pneumography (IP) is a non-invasive respiration measurement technique. Emerging applications of IP in respiratory medicine use the measured signal to monitor pulmonary flow and volume parameters related to airway obstruction during tidal breathing (TB). This requires a high impedance change (ΔZ)-to-lung volume change (ΔV) linearity. Four potential electrode configurations were tested on 10 healthy subjects. Only the novel configuration where the electrodes were placed in both the thorax and the arms yielded a highly linear ΔZ/ΔV in all subjects. The presented electrode configuration may expand the clinical use of IP from the conventional tidal volume estimation to flow measurement.