Functional coupling between the cortex and muscle is commonly quantified by cortico-muscular coherence (CMC) between electroencephalogram (EEG) and electromyogram (EMG) signals. However, the presence of noise in EEG and EMG often degrades CMC, making it challenging to detect: some healthy subjects with good motor skills show no significant CMC. This study proposes an approach based on structured errors-in-variables (EIV) modelling to estimate components of the cortex and muscle signals involved in movement control from noisy EEG and EMG signals for the purpose of coherence estimation. We describe three algorithms to identify the underlying EIV system: one based on total least squares; the other two on structured total least squares, in which the Toeplitz data matrix structure is preserved. The effectiveness of the proposed method is assessed using simulated and neurophysiological data, where it achieved considerable improvements in coherence levels.

MOTIVATION: Cell-type-specific gene expression is maintained in large part by transcription factors (TFs) selectively binding to distinct sets of sites in different cell types. Recent research works have provided evidence that such cell-type-specific binding is determined by TF's intrinsic sequence preferences, cooperative interactions with co-factors, cell-type-specific chromatin landscapes and 3D chromatin interactions. However, computational prediction and characterization of cell-type-specific and shared binding sites is rarely studied. RESULTS: In this article, we propose two computational approaches for predicting and characterizing cell-type-specific and shared binding sites by integrating multiple types of features, in which one is based on XGBoost and another is based on convolutional neural network (CNN). To validate the performance of our proposed approaches, ChIP-seq datasets of 10 binding factors were collected from the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines, each of which was further categorized into cell-type-specific (GM12878- and K562-specific) and shared binding sites. Then, multiple types of features for these binding sites were integrated to train the XGBoost- and CNN-based models. Experimental results show that our proposed approaches significantly outperform other competing methods on three classification tasks. Moreover, we identified independent feature contributions for cell-type-specific and shared sites through SHAP values and explored the ability of the CNN-based model to predict cell-type-specific and shared binding sites by excluding or including DNase signals. Furthermore, we investigated the generalization ability of our proposed approaches to different binding factors in the same cellular environment. AVAILABILITY AND IMPLEMENTATION: The source code is available at: https://github.com/turningpoint1988/CSSBS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Anxiety is a complex emotional state that has a great impact on people's physical and mental health. Effectively identifying different anxiety states is very important. By inducing various anxiety states of 12 healthy college students with electroencephalograph (EEG) recording, comprehensive EEG features, including not only commonly used frequency domain features but also the time domain, statistical and nonlinear features were extracted from different EEG bands and brain locations. Next, correlation analysis was performed between various features and anxiety level changes that were predetermined at each stage of the experiment using a 5-point Likert scale, and the most relevant features were collected. Then, different classifiers were applied to classify four anxiety levels using different features alone or together to explore their anxiety recognition ability. Based on our dataset, the highest accuracy of identifying four anxiety states reached approximately 62.56 percent using the Support Vector Machine (SVM), which improved the classification accuracy compared with previous studies. The results also revealed the importance of EEG linear features (especially for features including total power, mean square and variance) in anxiety recognition. Furthermore, it suggested that EEG features in the beta band and the frontal lobe contributed to anxiety recognition more than the features in the other bands or other brain locations. In short, this study improves the accuracy of multi-level anxiety recognition and helps in choosing better features for anxiety recognition, which lay the foundation for the detection of continuous anxiety changes.

Identifying and evaluating functionally connected regions in the brain has become a challenging problem to solve in many studies of neurological and psychiatric disorders. In particular, functional connectivity of brain mechanisms underlying disturbed cognition in depression is still not well understood in current neuroscience research. Based on the Stroop paradigm, specifically, the face-word Stroop task, we aimed to analyze task-based electroencephalography (EEG) functional connectivity in subjects with depression and in healthy controls, using concepts from time series clustering. In this study, EEG signals of 10 healthy subjects and 10 depressive patients were collected. Then EEG signals were segmented into temporal window corresponding to the event-related potentials (ERPs). For each duration, hierarchical clustering (HC) along with optimizations for the dynamic time warping (DTW) were employed to identify meaningful functionally connected regions and examine changes in depression. It was demonstrated that our method had the potential to become a useful tool for clinical investigators to identify the underlying impairments of brain functional connections in the patients with depression. One of the most representative functional connections obtained in the present study indicated that during the N450 component, the left and right frontal brain parts may discriminate depressive patients from healthy controls. This finding was interpreted by valence-hypothesis, which can prove the validity of the theory of emotional conflict in major depression.

Depression is a mental disorder of high prevalence, leading to a negative effect on individuals, their families, society and the economy. In recent years, the problem of automatic detection of depression from the speech signal has gained more interest. In this paper, a new multiple classifier system for depression recognition was developed and tested. The novel aspect of this methodology is the combination of different speech types and emotions. First of all, using a sample of 74 subjects (37 depressed patients and 37 healthy controls), we examined the discriminative power of different speech types (interview, picture description, and reading) and speech emotions (positive, neutral, and negative). Some voice features (e.g. short time energy, intensity, loudness, zero-crossing rate (ZCR), F0, jitter, shimmer, formants, mel frequency cepstral coefficients (MFCC), linear prediction coefficient (LPC), line spectrum pair (LSP), and perceptual linear predictive coefficients (PLP)) were tested. Then, a new multiple classifier method was proposed to detect depression. It was observed that the overall recognition rate using interview speech was higher than employing picture description speech and reading speech. Furthermore, neutral speech showed better performance than positive and negative speech. Among these features, short time energy, ZCR, LPC, MFCC and LSP were the robust features that gave high accuracy in different types of speech. Finally, this new approach showed a high accuracy of 78.02%, giving high encouragement for detecting depression in speech.