Correction to: Bacomics: a comprehensive cross area originating in the studies of various brain-apparatus conversations.

[This corrects the article DOI: 10.1007/s11571-020-09577-7.].

Rereferencing of clinical EEGs with nonunipolar mastoid reference to infinity reference by REST.

OBJECTIVE: Conventional electroencephalography (EEG) offline subtraction rereferencing is invalid for many clinical practices when adopting a specific nonunipolar recording montage (e.g., the ipsilateral mastoid (IM) and contralateral mastoid (CM)). Further comparative analyses would thus be blocked due to the lack of a uniform offline reference. Therefore, our goal was to resolve this problem by introducing and assessing the reference electrode standardization technique (REST) to transform nonunipolar mastoid montages into a computational zero reference at infinity (IR) offline. METHODS: For EEG signals and power/connectivity configurations, simulation and clinical schizophrenia resting-state EEG datasets were used to investigate the performance of REST. RESULTS: REST produced small absolute errors (signal level: 1.21-1.26; power: 0.0057-0.021; connectivity: 0.066-0.088) and high correlations (>0.9) between the IM/CM-IR and true IR references. Using clinical data with the IM online reference, REST revealed valuable changes in spectral and connectivity (P < 0.05) in schizophrenia patients, consistent with previous studies. CONCLUSIONS: These results demonstrated that REST transformation could be adopted to resolve the offline rereferencing of clinical EEGs with specific nonunipolar mastoid references. SIGNIFICANCE: REST could be an effective and robust resolution for nonunipolar clinical EEGs and could therefore retrieve these data for further analysis by deriving a favorable offline reference IR.

Quantitative signal quality assessment for large-scale continuous scalp electroencephalography from a big data perspective.

Objective. Despite electroencephalography (EEG) being a widely used neuroimaging technique with an excellent temporal resolution, in practice, the signals are heavily contaminated by artifacts masking responses of interest in an experiment. It is thus essential to guarantee a prompt and effective detection of artifacts that provides quantitative quality assessment (QA) on raw EEG data. This type of pipeline is crucial for large-scale EEG studies. However, current EEG QA studies are still limited.Approach. In this study, combined from a big data perspective, we therefore describe a quantitative signal quality assessment pipeline, a stable and general threshold-based QA pipeline that automatically integrates artifact detection and new QA measures to assess continuous resting-state raw EEG data. One simulation dataset and two resting-state EEG datasets from 42 healthy subjects and 983 clinical patients were utilized to calibrate the QA pipeline.Main Results. The results demonstrate that (1) the QA indices selected are sensitive: they almost strictly and linearly decrease as the noise level increases; (2) stable, replicable QA thresholds are valid for other experimental and clinical EEG datasets; and (3) use of the QA pipeline on these datasets reveals that high-frequency noises are the most common noises in EEG practice. The QA pipeline is also deployed in the WeBrain cloud platform (https://webrain.uestc.edu.cn/, the Chinese EEG Brain Consortium portal).Significance. These findings suggest that the proposed QA pipeline may be a stable and promising approach for quantitative EEG signal quality assessment in large-scale EEG studies.

Reference Electrode Standardization Interpolation Technique (RESIT): A Novel Interpolation Method for Scalp EEG.

"Bad channels" are common phenomena during scalp electroencephalography (EEG) recording that arise due to various technique-related reasons, and reconstructing signals from bad channels is an inevitable choice in EEG processing. However, current interpolation methods are all based on purely mathematical interpolation theory, ignoring the neurophysiological basis of the EEG signals, and their performance needs to be further improved, especially when there are many scattered or adjacent bad channels. Therefore, a new interpolation method, named the reference electrode standardization interpolation technique (RESIT), was developed for interpolating scalp EEG channels. Resting-state and event-related EEG datasets were used to investigate the performance of the RESIT. The main results showed that (1) assuming 10% bad channels, RESIT can reconstruct the bad channels well; (2) as the percentage of bad channels increased (from 2% to 85%), the absolute and relative errors between the true and RESIT-reconstructed signals generally increased, and the correlations between the true and RESIT signals decreased; (3) for a range of bad channel percentages (2% ~ 85%), the RESIT had lower absolute error (approximately 2.39% ~ 33.5% reduction), lower relative errors (approximately 1.3% ~ 35.7% reduction) and higher correlations (approximately 2% ~ 690% increase) than traditional interpolation methods, including neighbor interpolation (NI) and spherical spline interpolation (SSI). In addition, the RESIT was integrated into the EEG preprocessing pipeline on the WeBrain cloud platform ( https://webrain.uestc.edu.cn/ ). These results suggest that the RESIT is a promising interpolation method for both separate and simultaneous EEG preprocessing that benefits further EEG analysis, including event-related potential (ERP) analysis, EEG network analysis, and strict group-level statistics.

Bacomics: a comprehensive cross area originating in the studies of various brain-apparatus conversations.

The brain is the most important organ of the human body, and the conversations between the brain and an apparatus can not only reveal a normally functioning or a dysfunctional brain but also can modulate the brain. Here, the apparatus may be a nonbiological instrument, such as a computer, and the consequent brain-computer interface is now a very popular research area with various applications. The apparatus may also be a biological organ or system, such as the gut and muscle, and their efficient conversations with the brain are vital for a healthy life. Are there any common bases that bind these different scenarios? Here, we propose a new comprehensive cross area: Bacomics, which comes from brain-apparatus conversations (BAC) + omics. We take Bacomics to cover at least three situations: (1) The brain is normal, but the conversation channel is disabled, as in amyotrophic lateral sclerosis. The task is to reconstruct or open up new channels to reactivate the brain function. (2) The brain is in disorder, such as in Parkinson's disease, and the work is to utilize existing or open up new channels to intervene, repair and modulate the brain by medications or stimulation. (3) Both the brain and channels are in order, and the goal is to enhance coordinated development between the brain and apparatus. In this paper, we elaborate the connotation of BAC into three aspects according to the information flow: the issue of output to the outside (BAC-1), the issue of input to the brain (BAC-2) and the issue of unity of brain and apparatus (BAC-3). More importantly, there are no less than five principles that may be taken as the cornerstones of Bacomics, such as feedforward and feedback control, brain plasticity, harmony, the unity of opposites and systems principles. Clearly, Bacomics integrates these seemingly disparate domains, but more importantly, opens a much wider door for the research and development of the brain, and the principles further provide the general framework in which to realize or optimize these various conversations.

A Comparative Study of Different EEG Reference Choices for Event-Related Potentials Extracted by Independent Component Analysis.

In the event-related potential (ERP) of scalp electroencephalography (EEG) studies, the vertex reference (Cz), linked mastoids or ears (LM), and average reference (AVG) are popular reference methods, and the reference electrode standardization technique (REST) is increasingly applied. Because scalp EEG recordings are considered as spatially degraded signals, independent component analysis (ICA) is a widely used data-driven method for obtaining ERPs by decomposing EEG data. However, the accurate estimation of the differences in ERP components extracted by ICA with different references remains unclear. In this study, we first provided formal descriptions of the above reference methods (Cz, LM, AVG, and REST) and ICA decomposition in ERP and then investigated the influences of different reference techniques on simulation and real EEG datasets. The results revealed that (1) the reference method did not change the peak amplitudes and latencies of relative ERPs corresponding to some IC time courses; (2) there were non-negligible effects of different reference methods on both temporal ERPs and spatial topographies of some ICs; and (3) compared to Cz, LM, and AR, considering both the performances of temporal ERPs and spatial topographies, the REST reference had overall superiority. These findings provide a recommended choice of REST for ICA analysis at the trial level and contribute to empirical investigations regarding the use of reference methods in ERP domains with ICA analysis.

The Effects of Music Intervention on Functional Connectivity Strength of the Brain in Schizophrenia.

Schizophrenia is often associated with behavior abnormality in the cognitive and affective domain. Music intervention is used as a complementary treatment for improving symptoms in patients with schizophrenia. However, the neurophysiological correlates of these remissions remain poorly understood. Here, we investigated the effects of music intervention in neural circuits through functional magnetic resonance imaging (fMRI) study in schizophrenic subjects. Under the standard care, patients were randomly assigned to music and non-music interventions (MTSZ, UMTSZ) for 1 month. Resting-state fMRI were acquired over three time points (baseline, 1 month, and 6 months later) in patients and analyzed using functional connectivity strength (FCS) and seed-based functional connection (FC) approaches. At baseline, compared with healthy controls, decreased FCS in the right middle temporal gyrus (MTG) was observed in patients. However, after music intervention, the functional circuitry of the right MTG, which was related with the function of emotion and sensorimotor, was improved in MTSZ. Furthermore, the FC increments were significantly correlated with the improvement of symptoms, while vanishing 6 months later. Together, these findings provided evidence that music intervention might positively modulate the functional connectivity of MTG in patients with schizophrenia; such changes might be associated with the observed therapeutic effects of music intervention on neurocognitive function. This trial is registered with ChiCTR-OPC-14005339.

Detection of the type III secretion system and its phylogenetic and symbiotic characterization in peanut bradyrhizobia isolated from Guangdong Province, China.

The distribution of rhcRST and rhcJ-C1 fragments located in different loci of the type III secretion system (T3SS) gene cluster in the peanut-nodulating bradyrhizobia isolated from Guangdong Province, China was investigated by PCR-based sequencing. T3SS was detected in approximately one-third of the peanut bradyrhizobial strains and the T3SS-harboring strains belonging to different Bradyrhizobium genomic species. Diverse T3SS groups corresponding to different symbiotic gene types were defined among the 23 T3SS-harboring strains. The same or similar T3SS genes were detected in different genospecies, indicating that interspecies horizontal transfer of symbiotic genes had occurred in the Bradyrhizobium genus.

How do reference montage and electrodes setup affect the measured scalp EEG potentials?

OBJECTIVE: Human scalp electroencephalogram (EEG) is widely applied in cognitive neuroscience and clinical studies due to its non-invasiveness and ultra-high time resolution. However, the representativeness of the measured EEG potentials for the underneath neural activities is still a problem under debate. This study aims to investigate systematically how both reference montage and electrodes setup affect the accuracy of EEG potentials. APPROACH: First, the standard EEG potentials are generated by the forward calculation with a single dipole in the neural source space, for eleven channel numbers (10, 16, 21, 32, 64, 85, 96, 128, 129, 257, 335). Here, the reference is the ideal infinity implicitly determined by forward theory. Then, the standard EEG potentials are transformed to recordings with different references including five mono-polar references (Left earlobe, Fz, Pz, Oz, Cz), and three re-references (linked mastoids (LM), average reference (AR) and reference electrode standardization technique (REST)). Finally, the relative errors between the standard EEG potentials and the transformed ones are evaluated in terms of channel number, scalp regions, electrodes layout, dipole source position and orientation, as well as sensor noise and head model. MAIN RESULTS: Mono-polar reference recordings are usually of large distortions; thus, a re-reference after online mono-polar recording should be adopted in general to mitigate this effect. Among the three re-references, REST is generally superior to AR for all factors compared, and LM performs worst. REST is insensitive to head model perturbation. AR is subject to electrodes coverage and dipole orientation but no close relation with channel number. SIGNIFICANCE: These results indicate that REST would be the first choice of re-reference and AR may be an alternative option for high level sensor noise case. Our findings may provide the helpful suggestions on how to obtain the EEG potentials as accurately as possible for cognitive neuroscientists and clinicians.

How do the reference montage and electrodes setup affect the measured scalp EEG potentials?

OBJECTIVE: Human scalp electroencephalogram (EEG) is widely applied in cognitive neuroscience and clinical studies due to its non-invasiveness and ultra-high time resolution. However, the representativeness of the measured EEG potentials for the underneath neural activities is still a problem under debate. This study aims to investigate systematically how both reference montage and electrodes setup affect the accuracy of EEG potentials. APPROACH: First, the standard EEG potentials are generated by the forward calculation with a single dipole in the neural source space, for eleven channel numbers (10, 16, 21, 32, 64, 85, 96, 128, 129, 257, 335). Here, the reference is the ideal infinity implicitly determined by forward theory. Then, the standard EEG potentials are transformed to recordings with different references including five monopolar references (Left earlobe, Fz, Pz, Oz, Cz), and three re-references (Linked Mastoids (LM), Average Reference (AR) and Reference Electrode Standardization Technique (REST)). Finally, the relative errors between the standard EEG potentials and the transformed ones are evaluated in terms of channel number, scalp regions, electrodes layout, dipole source position and orientation, as well as sensor noise and head model. MAIN RESULTS: Mono-polar reference recordings are usually of large distortions; thus, a re-reference after online mono-polar recording should be adopted in general to mitigate this effect. Among the three re-references, REST is generally superior to AR for all factors compared, and LM performs worst. REST is insensitive to head model perturbation. AR is subject to electrodes coverage and dipole orientation but no close relation with channel number. SIGNIFICANCE: These results indicate that REST would be the first choice of re-reference and AR may be an alternative option for high level sensor noise case. Our findings may provide the helpful suggestions on how to obtain the EEG potentials as accurately as possible for cognitive neuroscientists and clinicians.

MATLAB Toolboxes for Reference Electrode Standardization Technique (REST) of Scalp EEG.

Reference electrode standardization technique (REST) has been increasingly acknowledged and applied as a re-reference technique to transform an actual multi-channels recordings to approximately zero reference ones in electroencephalography/event-related potentials (EEG/ERPs) community around the world in recent years. However, a more easy-to-use toolbox for re-referencing scalp EEG data to zero reference is still lacking. Here, we have therefore developed two open-source MATLAB toolboxes for REST of scalp EEG. One version of REST is closely integrated into EEGLAB, which is a popular MATLAB toolbox for processing the EEG data; and another is a batch version to make it more convenient and efficient for experienced users. Both of them are designed to provide an easy-to-use for novice researchers and flexibility for experienced researchers. All versions of the REST toolboxes can be freely downloaded at http://www.neuro.uestc.edu.cn/rest/Down.html, and the detailed information including publications, comments and documents on REST can also be found from this website. An example of usage is given with comparative results of REST and average reference. We hope these user-friendly REST toolboxes could make the relatively novel technique of REST easier to study, especially for applications in various EEG studies.

A Comparative Study on the Dynamic EEG Center of Mass with Different References.

One of the most fundamental issues during an EEG study is choosing an available neutral reference. The infinity zero reference obtained by the reference electrode standardization technique (REST) has been recommended and used for its higher accuracy. This paper examined three traditional references, the average reference (AR), the linked mastoids reference (LM), and REST, in the study of the EEG center of mass (CM) using simulated and real ERPs. In the simulation, the relative error of REST was the smallest among the references. As for the ERP data with the visual oddball paradigm, the dynamic CM trajectory and its traveling velocity obtained by REST characterized three typical stages in spatial domain and temporal speed metrics, which provided useful information in addition to the distinct ERP waveform in the temporal domain. The results showed that the CM traveling from the frontal to parietal areas corresponding to the earlier positive components (i.e., P200 and P250), stays temporarily at the parietal area corresponding to P300 and then returns to the frontal area during the recovery stage. Compared with REST, AR, and LM not only changed the amplitude of P300 significantly but distorted the CM trajectory and its instantaneous velocity. As REST continues to provide objective results, we recommend that REST be used in future EEG/ERP CM studies.

Music Intervention Leads to Increased Insular Connectivity and Improved Clinical Symptoms in Schizophrenia.

Schizophrenia is a syndrome that is typically accompanied by delusions and hallucinations that might be associated with insular pathology. Music intervention, as a complementary therapy, is commonly used to improve psychiatric symptoms in the maintenance stage of schizophrenia. In this study, we employed a longitudinal design to assess the effects of listening to Mozart music on the insular functional connectivity (FC) in patients with schizophrenia. Thirty-six schizophrenia patients were randomly divided into two equal groups as follows: the music intervention (MTSZ) group, which received a 1-month music intervention series combined with antipsychotic drugs, and the no-music intervention (UMTSZ) group, which was treated solely with antipsychotic drugs. Resting-state functional magnetic resonance imaging (fMRI) scans were performed at the following three timepoints: baseline, 1 month after baseline and 6 months after baseline. Nineteen healthy participants were recruited as controls. An FC analysis seeded in the insular subregions and machine learning techniques were used to examine intervention-related changes. After 1 month of listening to Mozart music, the MTSZ showed increased FC in the dorsal anterior insula (dAI) and posterior insular (PI) networks, including the dAI-ACC, PI-pre/postcentral cortices, and PI-ACC connectivity. However, these enhanced FCs had vanished in follow-up visits after 6 months. Additionally, a support vector regression on the FC of the dAI-ACC at baseline yielded a significant prediction of relative symptom remission in response to music intervention. Furthermore, the validation analyses revealed that 1 month of music intervention could facilitate improvement of the insular FC in schizophrenia. Together, these findings revealed that the insular cortex could potentially be an important region in music intervention for patients with schizophrenia, thus improving the patients' psychiatric symptoms through normalizing the salience and sensorimotor networks.

Functional abnormalities of the right posterior insula are related to the altered self-experience in schizophrenia.

The insula is involved in detecting the salience of internal and external stimuli, and it plays a critical role in psychosis. Previous studies have demonstrated the structural and functional alterations of the insula in schizophrenia. To acquire a full picture of the functional alterations of the insula in schizophrenia, the resting-state fMRI data of 46 patients with schizophrenia and 46 healthy control subjects were collected. We used clustering analysis to divide the insula into three subregions: the dorsal anterior insula (dAI), ventral anterior insula (vAI) and posterior insula (PI). Then, whole-brain functional connectivity analysis was conducted based on these subregions. The results showed that the right dAI and PI in patients exhibited altered functional connections with the primary sensorimotor area. In addition, the right PI of the patients exhibited increased functional correlations with the thalamus. More importantly, the altered functional properties of the right PI were significantly correlated with the severity of the delusion and poor insight in schizophrenia. The results suggested that the right PI might play an important role in self-experience processing in schizophrenia. Accordingly, the right PI should be considered very important in the pathological mechanism of schizophrenia.

Altered Local Spontaneous Brain Activity in Juvenile Myoclonic Epilepsy: A Preliminary Resting-State fMRI Study.

Purpose. The purpose of this study was to evaluate the regional synchronization of brain in patients with juvenile myoclonic epilepsy (JME). Methods. Resting-state fMRI data were acquired from twenty-one patients with JME and twenty-two healthy subjects. Regional homogeneity (ReHo) was used to analyze the spontaneous activity in whole brain. Two-sample t-test was performed to detect the ReHo difference between two groups. Correlations between the ReHo values and features of seizures were calculated further. Key Findings. Compared with healthy controls, patients showed significantly increased ReHo in bilateral thalami and motor-related cortex regions and a substantial reduction of ReHo in cerebellum and occipitoparietal lobe. In addition, greater ReHo value in the left paracentral lobule was linked to the older age of onset in patients. Significance. These findings implicated the abnormality of thalamomotor cortical network in JME which were associated with the genesis and propagation of epileptiform activity. Moreover, our study supported that the local brain spontaneous activity is a potential tool to investigate the epileptic activity and provided important insights into understanding the pathophysiological mechanisms of JME.

Altered Basal Ganglia Network Integration in Schizophrenia.

UNLABELLED: The basal ganglia involve in a range of functions that are disturbed in schizophrenia patients. This study decomposed the resting-state data of 28 schizophrenia patients and 31 healthy controls with spatial independent component analysis and identified increased functional integration in the bilateral caudate nucleus in schizophrenia patients. Further, the caudate nucleus in patients showed altered functional connection with the prefrontal area and cerebellum. These results identified the importance of basal ganglia in schizophrenia patients. CLINICAL TRIAL REGISTRATION: Chinese Clinical Trial Registry. Registration number ChiCTR-RCS-14004878.

Functional disconnection between the visual cortex and the sensorimotor cortex suggests a potential mechanism for self-disorder in schizophrenia.

UNLABELLED: Self-disorder is a hallmark characteristic of schizophrenia. This deficit may stem from an inability to efficiently integrate multisensory bodily signals. Twenty-nine schizophrenia patients and thirty-one healthy controls underwent resting-state fMRI in this study. A data-driven method, functional connectivity density mapping (FCD), was used to investigate cortical functional connectivity changes in the patients. Areas with significantly different FCD were chosen to calculate functional connectivity maps. The schizophrenia patients exhibited increased local FCD in frontal areas while demonstrating decreased local FCD in the primary sensorimotor area and in the occipital lobe. The functional connectivity analysis illustrated decreased functional connectivity between visual areas and the primary sensorimotor area. These findings suggest disturbed integration in perception-motor processing, which may contribute to mapping the neural physiopathology associated with self-disorder in schizophrenia patients. CLINICAL TRIAL REGISTRATION: Chinese Clinical Trial Registry. Registration number. ChiCTR-RCS-14004878.

Identifying enhanced cortico-basal ganglia loops associated with prolonged dance training.

Studies have revealed that prolonged, specialized training combined with higher cognitive conditioning induces enhanced brain alternation. In particular, dancers with long-term dance experience exhibit superior motor control and integration with their sensorimotor networks. However, little is known about the functional connectivity patterns of spontaneous intrinsic activities in the sensorimotor network of dancers. Our study examined the functional connectivity density (FCD) of dancers with a mean period of over 10 years of dance training in contrast with a matched non-dancer group without formal dance training using resting-state fMRI scans. FCD was mapped and analyzed, and the functional connectivity (FC) analyses were then performed based on the difference of FCD. Compared to the non-dancers, the dancers exhibited significantly increased FCD in the precentral gyri, postcentral gyri and bilateral putamen. Furthermore, the results of the FC analysis revealed enhanced connections between the middle cingulate cortex and the bilateral putamen and between the precentral and the postcentral gyri. All findings indicated an enhanced functional integration in the cortico-basal ganglia loops that govern motor control and integration in dancers. These findings might reflect improved sensorimotor function for the dancers consequent to long-term dance training.

Long-term effects of musical training and functional plasticity in salience system.

Musicians undergoing long-term musical training show improved emotional and cognitive function, which suggests the presence of neuroplasticity. The structural and functional impacts of the human brain have been observed in musicians. In this study, we used data-driven functional connectivity analysis to map local and distant functional connectivity in resting-state functional magnetic resonance imaging data from 28 professional musicians and 28 nonmusicians. Compared with nonmusicians, musicians exhibited significantly greater local functional connectivity density in 10 regions, including the bilateral dorsal anterior cingulate cortex, anterior insula, and anterior temporoparietal junction. A distant functional connectivity analysis demonstrated that most of these regions were included in salience system, which is associated with high-level cognitive control and fundamental attentional process. Additionally, musicians had significantly greater functional integration in this system, especially for connections to the left insula. Increased functional connectivity between the left insula and right temporoparietal junction may be a response to long-term musical training. Our findings indicate that the improvement of salience network is involved in musical training. The salience system may represent a new avenue for exploration regarding the underlying foundations of enhanced higher-level cognitive processes in musicians.

Probabilistic diffusion tractography reveals improvement of structural network in musicians.

PURPOSE: Musicians experience a large amount of information transfer and integration of complex sensory, motor, and auditory processes when training and playing musical instruments. Therefore, musicians are a useful model in which to investigate neural adaptations in the brain. METHODS: Here, based on diffusion-weighted imaging, probabilistic tractography was used to determine the architecture of white matter anatomical networks in musicians and non-musicians. Furthermore, the features of the white matter networks were analyzed using graph theory. RESULTS: Small-world properties of the white matter network were observed in both groups. Compared with non-musicians, the musicians exhibited significantly increased connectivity strength in the left and right supplementary motor areas, the left calcarine fissure and surrounding cortex and the right caudate nucleus, as well as a significantly larger weighted clustering coefficient in the right olfactory cortex, the left medial superior frontal gyrus, the right gyrus rectus, the left lingual gyrus, the left supramarginal gyrus, and the right pallidum. Furthermore, there were differences in the node betweenness centrality in several regions. However, no significant differences in topological properties were observed at a global level. CONCLUSIONS: We illustrated preliminary findings to extend the network level understanding of white matter plasticity in musicians who have had long-term musical training. These structural, network-based findings may indicate that musicians have enhanced information transmission efficiencies in local white matter networks that are related to musical training.