A new approach to sample entropy of multi-channel signals: application to EEG signals

In this paper, we propose a new algorithm to calculate sample entropy of multivariate data. Over the existing method, the one proposed here has the advantage of maintaining good results as the number of channels increases. The new and already-existing algorithms were applied on multivariate white Gaussian noise signals, pink noise signals, and mixtures of both. For high number of channels, the existing method failed to show that white noise is always the most irregular whereas the proposed method always had the entropy of white noise the highest. Application of both algorithms on MIX process signals also confirmed the ability of the proposed method to handle larger number of channels without risking erroneous results. We also applied the proposed algorithm on EEG data from epileptic patients before and after treatments. The results showed an increase in entropy values after treatment in the regions where the focus was localized. This goes in the same way as the medical point of view that indicated a better health state for these patients

Time-varying time-frequency complexity measures for epileptic EEG data analysis

Objective: Our goal is to use existing and to propose new time-frequency entropy measures that objectively evaluate the improvement on epileptic patients after medication by studying their resting state EEG recordings. An increase in the complexity of the signals would confirm an improvement in the general state of the patient. Methods: We review the Rényi entropy based on time-frequency representations, along with its time-varying version. We also discuss the entropy based on singular value decomposition computed from a time-frequency representation, and introduce its corresponding time-dependant version. We test these quantities on synthetic data. Friedman tests are used to confirm the differences between signals (before and after proper medication). Principal component analysis is used for dimensional reduction prior to a simple threshold discrimination. Results: Experimental results show a consistent increase in complexity measures in the different regions of the brain. These findings suggest that extracted features can be used to monitor treatment. When combined, they are useful for classification purposes, with areas under ROC curves higher than 0.93 in some regions. Conclusion: Here we applied time-frequency complexity measures to resting state EEG signals from epileptic patients for the first time. We also introduced a new time-varying complexity measure. We showed that these features are able to evaluate the treatment of the patient, and to perform classification. Significance: The time-frequency complexities, and their time-varying versions, can be used to monitor the treatment of epileptic patients. They could be applied to a wider range of problems

Loss of microbial topography between oral and nasopharyngeal microbiota and development of respiratory infections early in life

Rationale: The respiratory microbiota is increasingly being appreciated as an important mediator in the susceptibility to childhood respiratory tract infections (RTIs). Pathogens are presumed to originate from the nasopharyngeal ecosystem. Objectives: To investigate the association between early life respiratory microbiota and development of childhood RTIs. Methods: In a prospective birth cohort (Microbiome Utrecht Infant Study: MUIS), we characterized the oral microbiota longitudinally from birth until 6 months of age of 112 infants (nine regular samples/subject) and compared them with nasopharyngeal microbiota using 16S-rRNA–based sequencing. We also characterized oral and nasopharynx samples during RTI episodes in the first half year of life. Measurements and Main Results: Oral microbiota were driven mostly by feeding type, followed by age, mode of delivery, and season of sampling. In contrast to our previously published associations between nasopharyngeal microbiota development and susceptibility to RTIs, oral microbiota development was not directly associated with susceptibility to RTI development. However, we did observe an influx of oral taxa, such as Neisseria lactamica, Streptococcus, Prevotella nanceiensis, Fusobacterium, and Janthinobacterium lividum, in the nasopharyngeal microbiota before and during RTIs, which was accompanied by reduced presence and abundance of Corynebacterium, Dolosigranulum, and Moraxella spp. Moreover, this phenomenon was accompanied by reduced niche differentiation indicating loss of ecological topography preceding confirmed RTIs. This loss of ecological topography was further augmented by start of daycare, and linked to consecutive development of symptomatic infections. Conclusions: Together, our results link the loss of topography to subsequent development of RTI episodes. This may lead to new insights for prevention of RTIs and antibiotic use in childhood

Multivariate improved weighted multi-scale permutation entropy and its application on EEG data

This paper introduces an entropy based method that measures complexity in non-stationary multivariate signals. This method, called Mutivariate Improved Weighted Multiscale Permutation Entropy (mvIWMPE), has two main advantages: (i) it shows lower variance for the results when applied on a wide range of multivariate signals; (ii) it has good accuracy quantifying complexity of different recorded states in signals and hence discriminating them. mvIWMPE is based on two previously introduced permutation entropy algorithms, Improved Multiscale Permutation Entropy (IMPE) and Multivariate Weighted Mul-tiscale Permutation Entropy (mvWMPE). It combines the concept of coarse graining from IMPE and the introduction of the weight of amplitudes of the signals from mvWMPE. mvIWMPE was validated on both synthetic and human electroencephalographic (EEG) signals. Several synthetic signals were simulated: mixtures of white Gaussian noise (WGN) and pink noise, chaotic and convergent Lorenz system signals, stochastic and deterministic signals. As for real signals, resting-state EEG recorded in healthy and epileptic children during eyes closed and eyes open sessions were analyzed. Our method was compared to multivariate multiscale, multivariate weighted multiscale and multivariate improved multiscale permutation entropy methods. Performance on synthetic as well as on EEG signals showed more undeviating results and higher ability for mvIWMPE discriminating different states of signals (chaotic vs convergent, WGN vs pink noise, stochastic vs deterministic simulated signals, and eyes open vs eyes closed EEG signals). We herein proposed an efficient method to measure the complexity of multivariate non-stationary signals. Experimental results showed the accuracy and the robustness (in terms of variance) of the method

Benchmarking laboratory processes to characterise low-biomass respiratory microbiota

Abstract The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray–Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies