Data_Sheet_1_Emotion recognition based on microstate analysis from temporal and spatial patterns of electroencephalogram.PDF

IntroductionRecently, the microstate analysis method has been widely used to investigate the temporal and spatial dynamics of electroencephalogram (EEG) signals. However, most studies have focused on EEG at resting state, and few use microstate analysis to study emotional EEG. This paper aims to investigate the temporal and spatial patterns of EEG in emotional states, and the specific neurophysiological significance of microstates during the emotion cognitive process, and further explore the feasibility and effectiveness of applying the microstate analysis to emotion recognition.MethodsWe proposed a KLGEV-criterion-based microstate analysis method, which can automatically and adaptively identify the optimal number of microstates in emotional EEG. The extracted temporal and spatial microstate features then served as novel feature sets to improve the performance of EEG emotion recognition. We evaluated the proposed method on two publicly available emotional EEG datasets: the SJTU Emotion EEG Dataset (SEED) and the Database for Emotion Analysis using Physiological Signals (DEAP).ResultsFor the SEED dataset, 10 microstates were identified using the proposed method. These temporal and spatial features were fed into AutoGluon, an open-source automatic machine learning model, yielding an average three-class accuracy of 70.38% (±8.03%) in subject-dependent emotion recognition. For the DEAP dataset, the method identified 9 microstates. The average accuracy in the arousal dimension was 74.33% (±5.17%) and 75.49% (±5.70%) in the valence dimension, which were competitive performance compared to some previous machine-learning-based studies. Based on these results, we further discussed the neurophysiological relationship between specific microstates and emotions, which broaden our knowledge of the interpretability of EEG microstates. In particular, we found that arousal ratings were positively correlated with the activity of microstate C (anterior regions of default mode network) and negatively correlated with the activity of microstate D (dorsal attention network), while valence ratings were positively correlated with the activity of microstate B (visual network) and negatively correlated with the activity of microstate D (dorsal attention network).DiscussionIn summary, the findings in this paper indicate that the proposed KLGEV-criterion-based method can be employed to research emotional EEG signals effectively, and the microstate features are promising feature sets for EEG-based emotion recognition.</p

The average <i>d_N</i>/<i>d_S</i> ratio for the regions flanking polyQ tracts of different repeat sizes.

<p>The tracts were divided into three different groups. The first group of tracts included tracts of 4 or 5 glutamines, the second group consisted of tracts of 6–9 glutamines, and the third group comprised tracts of 10 or more glutamines.</p

Structural Basis for TatA Oligomerization: An NMR Study of <i>Escherichia coli</i> TatA Dimeric Structure

<div><p>Many proteins are transported across lipid membranes by protein translocation systems in living cells. The twin-arginine transport (Tat) system identified in bacteria and plant chloroplasts is a unique system that transports proteins across membranes in their fully-folded states. Up to date, the detailed molecular mechanism of this process remains largely unclear. The <i>Escherichia coli</i> Tat system consists of three essential transmembrane proteins: TatA, TatB and TatC. Among them, TatB and TatC form a tight complex and function in substrate recognition. The major component TatA contains a single transmembrane helix followed by an amphipathic helix, and is suggested to form the translocation pore via self-oligomerization. Since the TatA oligomer has to accommodate substrate proteins of various sizes and shapes, the process of its assembly stands essential for understanding the translocation mechanism. A structure model of TatA oligomer was recently proposed based on NMR and EPR observations, revealing contacts between the transmembrane helices from adjacent subunits. Herein we report the construction and stabilization of a dimeric TatA, as well as the structure determination by solution NMR spectroscopy. In addition to more extensive inter-subunit contacts between the transmembrane helices, we were also able to observe interactions between neighbouring amphipathic helices. The side-by-side packing of the amphipathic helices extends the solvent-exposed hydrophilic surface of the protein, which might be favourable for interactions with substrate proteins. The dimeric TatA structure offers more detailed information of TatA oligomeric interface and provides new insights on Tat translocation mechanism.</p></div

Characterization of the activity of MCG-TatA.

<p>A) Blue-native PAGE of wt-TatA, MCG-TatA and d-MCG-TatA. The mutant proteins retain the characteristic ladder pattern as the wild-type TatA. The molecular masses (kDa) of marker proteins are given on the left. B) Tenfold serial dilution of <i>ΔtatA</i> mutant strain expressing TatA variants on SDS-containing medium. The plates were anaerobically incubated at 35°C for 72 hours and then photographed (see more details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0103157#s2" target="_blank">Materials and Methods</a>). The upmost panel corresponds to a positive control experiment using the <i>ΔtatE</i> mutant strain transformed with empty pET-21a plasmids. The lower panel corresponds to the <i>ΔtatA</i> mutant strain transformed with either empty pET-21a plasmids or plasmids carrying wt-TatA gene or mutated variants.</p

Mean <i>dN/dS</i> ratios for region groups.

*<p>454 proteins contain poly-Q tracts of four or more glutamines in humans. However, this number excludes 41 human proteins without assigned homologs in either mouse or rat, which served as the references for estimating the <i>dN/dS</i> ratios. Additionally, the <i>dN/dS</i> ratios for some regions flanking the poly-Q tracts were not available by PAML estimation. The <i>dN/dS</i> ratios were calculated for a region including 33 amino acids on either side of the repeat and excluding the repeat.</p

Human serum enhances infectivity of DV.

<p>(A) U937, (B) PBMCs, (E) Huh7 and (F) HepG2 cells were infected with DV collected from infected Vero cells cultured in serum-free medium (DV/SFM) or DV/SFM containing 10% human serum (DV/HSM) at an MOI of 0.1. Total RNA was extracted at 1 dpi, 2 dpi, 3 dpi for infected U937 cells respectively, and at 1 dpi for other infected cells. Viral replication was measured by real-time PCR. The results represent the average standard deviation of three independent experiments. NS, no significance; *p<0.05; **p<0.01; ***p<0.001. (C) DV/SFM and DV/HSM were ultracentrifuged (UC) over a 30% sucrose cushion, and resulting virus pellets (UC DV/SFM and UC DV/HSM) were resuspended in serum-free medium followed by infection of PBMCs. At 3 dpi, virus infection of cells was observed by IFA and virus RNA copy number was measure by real-time PCR. (D) Detection of dengue IgG antibodies in human serum. Dengue IgG ELISA kit (<i>Abnova</i>) was used to measure dengue IgG antibodies in the human pooled serum, and results were presented as antibody index (Ab index) values, which were calculated by the value of OD450 of the tested sample divided by the cut-off value that was generated from the calibrator in the kit. Ab index <0.9, no detectable IgG antibody to DV; 0.9–1.1, borderline positive; >1.1, detectable IgG antibody to DV. Positive Control (CTL) and negative control (CTL) are supplied in the kit.</p

Co-precipitation of DV with ApoA-I.

<p>(A) Vero cells were infected with DV at a MOI of 1 and culture medium were changed to DMEM with 10% human serum HS (HSM) at 2 dpi. The mock-infected cells by DMEM was used as a control and also subjected to the same medium change. Culture supernatants were harvested at 7 dpi and purified by sucrose cushion ultracentrifugation (UC). The virus pellets were resuspended in serum-free DMEM. Presence of ApoA-I was analyzed by Western blotting using anti-ApoA-I antibody. (B) Human serum was added into DV/SFM to a final concentration of 10% and the mixture was incubated at 4° for 1 hour, followed by sucrose cushion ultracentrifugation. The pellets were analyzed by Western blotting using anti-ApoA-I and anti-E antibodies respectively. (C) Co-immunoprecipitation of ApoA-I with DV. AD-293 cells were transfected with a plasmid expressing FLAG-tagged ApoA-I (pApoAI-FLAG) and cultured in serum-free DMEM. At 3 dpt, secreted ApoA-I in the culture supernatant was purified with anti-FLAG M2 Affinity Gel. The resulting ApoAI-FLAG/M2 beads were washed twice with 1×TBS and incubated with DV/SFM at 4°C for over night. The co-immunoprecipitates were eluted and detected by Western blotting with anti-E and anti-FLAG antibodies. As a control, co-immunoprecipitation was also performed using the supernatant from cells transfected with empty vector p3×FLAG-CMV-14 (pFLAG). M, pre-stained protein marker.</p

2D ¹H-¹⁵N HSQC spectrum of d-MCG-TatA in DPC micelles annotated with the backbone assignments.

<p>The spectrum was collected on a Bruker Avance 800(with a cryo-probe) at 35°C and a DPR of 86. The assignments are labeled with the one-letter amino acid code and residue number. The side chain NH₂ peaks of Asn and Gln are connected by horizontal lines. The asterisk indicates residues of the N-terminal M(-3)C(-2)G(-1) extension and the C-terminal His-tag.</p

ApoA-I promotes DV attachment/entry.

<p>Huh-7 cells infected with DV/SFM, DV/HSM or DV/ApoAI-FLAG were harvested at 30 minutes postinfection. Dengue antigen on the surface of infected cells was detected by indirect immunofluorescence assay and the percentage of DV-bound cells was analyzed by FACS.</p

Solution structures of monomeric and dimeric TatA.

<p>A) Ensemble (left) and cartoon (right) representations of monomeric <i>E. coli</i> TatA structure. B) Ensemble (left) and cartoon (right) representations of dimeric <i>E. coli</i> TatA structure.</p