CRISPR-Cas is a tool that is widely used for gene editing. However, unexpected off-target effects may occur as a result of long-term nuclease activity. Anti-CRISPR proteins, which are powerful molecules that inhibit the CRISPR–Cas system, may have the potential to promote better utilization of the CRISPR-Cas system in gene editing, especially for gene therapy. Additionally, more in-depth research on these proteins would help researchers to better understand the co-evolution of bacteria and phages. Therefore, it is necessary to collect and integrate data on various types of anti-CRISPRs. Herein, data on these proteins were manually gathered through data screening of the literatures. Then, the first online resource, anti-CRISPRdb, was constructed for effectively organizing these proteins. It contains the available protein sequences, DNA sequences, coding regions, source organisms, taxonomy, virulence, protein interactors and their corresponding three-dimensional structures. Users can access our database at http://cefg.uestc.edu.cn/anti-CRISPRdb/ without registration. We believe that the anti-CRISPRdb can be used as a resource to facilitate research on anti-CRISPR proteins and in related fields.

A novel wavelet-based approach for medical image fusion is presented, which is developed by taking into not only account the characteristics of human visual system (HVS) but also the physical meaning of the wavelet coefficients. After the medical images to be fused are decomposed by the wavelet transform, different-fusion schemes for combining the coefficients are proposed: coefficients in low-frequency band are selected with a visibility-based scheme, and coefficients in high-frequency bands are selected with a variance based method. To overcome the presence of noise and guarantee the homogeneity of the fused image, all the coefficients are subsequently performed by a window-based consistency verification process. The fused image is finally constructed by the inverse wavelet transform with all composite coefficients. To quantitatively evaluate and prove the performance of the proposed method, series of experiments and comparisons with some existing fusion methods are carried out in the paper. Experimental results on simulated and real medical images indicate that the proposed method is effective and can get satisfactory fusion results.

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The organization of the brain functional network is associated with mental fatigue, but little is known about the brain network topology that is modulated by the mental fatigue. In this study, we used the graph theory approach to investigate reconfiguration changes in functional networks of different electroen-cephalography (EEG) bands from 16 subjects performing a simulated driving task. Behavior and brain functional networks were compared between the normal and driving mental fatigue states. The scores of subjective self-reports indicated that 90 min of simulated driving-induced mental fatigue. We observed that coherence was significantly increased in the frontal, central, and temporal brain regions. Furthermore, in the brain network topology metric, significant increases were observed in the clustering coefficient (Cp) for beta, alpha, and delta bands and the character path length (Lp) for all EEG bands. The normalized measures γ showed significant increases in beta, alpha, and delta bands, and λ showed similar patterns in beta and theta bands. These results indicate that functional network topology can shift the network topology structure toward a more economic but less efficient configuration, which suggests low wiring costs in functional networks and disruption of the effective interactions between and across cortical regions during mental fatigue states. Graph theory analysis might be a useful tool for further understanding the neural mechanisms of driving mental fatigue.

ABSTRACT. Essential genes are those genes that are needed by organisms at any time and under any conditions. It is very important for us to identify essential genes from bacterial genomes because of their vital role in synthetic biology and biomedical practices. In this paper, we developed a support vector machine (SVM)-based method to predict essential genes of bacterial genomes using only compositional features. These features are all derived from the primary sequences, i.e., nucleotide sequences and protein sequences. After training on the multiple samplings of the labeled (essential or not essential) features using a library for SVM, we obtained an average area under the ROC curve (AUC) of about 0.82 in a 5-fold cross-validation for Escherichia coli and about 0.74 for Mycoplasma pulmonis. We further evaluated the performance of the method proposed using the dataset consisting of 16 bacterial genomes, and an average AUC of 0.76 was achieved. Based on this training dataset, a model for essential gene prediction was established. Another two independent genomes, Shewanella oneidensis RW1 and Salmonella enterica serovar Typhimurium SL1344 were used to evalutate the model. Results showed that the AUC sores were 0.77 and 0.81, respectively. For the convenience of the vast majority Predicting bacterial essential genes by sequence composition of experimental scientists, a web server has been constructed, which is freely available at http://cefg.uestc.edu.cn:9999/egp.

A new machine learning method referred to as F-score_ELM was proposed to classify the lying and truth-telling using the electroencephalogram (EEG) signals from 28 guilty and innocent subjects. Thirty-one features were extracted from the probe responses from these subjects. Then, a recently-developed classifier called extreme learning machine (ELM) was combined with F-score, a simple but effective feature selection method, to jointly optimize the number of the hidden nodes of ELM and the feature subset by a grid-searching training procedure. The method was compared to two classification models combining principal component analysis with back-propagation network and support vector machine classifiers. We thoroughly assessed the performance of these classification models including the training and testing time, sensitivity and specificity from the training and testing sets, as well as network size. The experimental results showed that the number of the hidden nodes can be effectively optimized by the proposed method. Also, F-score_ELM obtained the best classification accuracy and required the shortest training and testing time.

The extraction of blood vessels from retinal images is an important and challenging task in medical analysis and diagnosis. This paper presents a novel hybrid automatic approach for the extraction of retinal image vessels. The method consists in the application of mathematical morphology and a fuzzy clustering algorithm followed by a purification procedure. In mathematical morphology, the retinal image is smoothed and strengthened so that the blood vessels are enhanced and the background information is suppressed. The fuzzy clustering algorithm is then employed to the previous enhanced image for segmentation. After the fuzzy segmentation, a purification procedure is used to reduce the weak edges and noise, and the final results of the blood vessels are consequently achieved. The performance of the proposed method is compared with some existing segmentation methods and hand-labeled segmentations. The approach has been tested on a series of retinal images, and experimental results show that our technique is promising and effective.

The concealed information test (CIT) has drawn much attention and has been widely investigated in recent years. In this study, a novel CIT method based on denoised P3 and machine learning was proposed to improve the accuracy of lie detection. Thirty participants were chosen as the guilty and innocent participants to perform the paradigms of 3 types of stimuli. The electroencephalogram (EEG) signals were recorded and separated into many single trials. In order to enhance the signal noise ratio (SNR) of P3 components, the independent component analysis (ICA) method was adopted to separate non-P3 components (i.e., artifacts) from every single trial. In order to automatically identify the P3 independent components (ICs), a new method based on topography template was proposed to automatically identify the P3 ICs. Then the P3 waveforms with high SNR were reconstructed on Pz electrodes. Second, the 3 groups of features based on time,frequency, and wavelets were extracted from the reconstructed P3 waveforms. Finally, 2 classes of feature samples were used to train a support vector machine (SVM) classifier because it has higher performance compared with several other classifiers. Meanwhile, the optimal number of P3 ICs and some other parameter values in the classifiers were determined by the cross-validation procedures. The presented method achieved a balance test accuracy of 84.29% on detecting P3 components for the guilty and innocent participants. The presented method improves the efficiency of CIT in comparison with previous reported methods.