An environment can be searched far more efficiently if the appropriate search strategy is used. Because of the limited individual abilities of swarm robots, namely, local sensing and low processing power, random searching is the main search strategy used in swarm robotics. The random walk methods that are used most commonly are Brownian motion and Lévy flight, both of which mimic the self-organized behavior of social insects. However, both methods are somewhat limited when applied to swarm robotics, where having the robots search repeatedly can result in highly inefficient searching. Therefore, by analyzing the characteristics of swarm robotic exploration, this paper proposes an improved random walk method in which each robot adjusts its step size adaptively to reduce the number of repeated searches by estimating the density of robots in the environment. Simulation experiments and experiments with actual robots are conducted to study the effectiveness of the proposed method and evaluate its performance in an exploration mission. The experimental results presented in this paper show that an area is covered more efficiently using the proposed method than it is using either Brownian motion or Lévy flight.

Bacteriophage virion proteins and non-virion proteins have distinct functions in biological processes, such as specificity determination for host bacteria, bacteriophage replication and transcription. Accurate identification of bacteriophage virion proteins from bacteriophage protein sequences is significant to understand the complex virulence mechanism in host bacteria and the influence of bacteriophages on the development of antibacterial drugs. In this study, an ensemble method for bacteriophage virion protein prediction from bacteriophage protein sequences is put forward with hybrid feature spaces incorporating CTD (composition, transition and distribution), bi-profile Bayes, PseAAC (pseudo-amino acid composition) and PSSM (position-specific scoring matrix). When performing on the training dataset 10-fold cross-validation, the presented method achieves a satisfactory prediction result with a sensitivity of 0.870, a specificity of 0.830, an accuracy of 0.850 and Matthew’s correlation coefficient (MCC) of 0.701, respectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous studies with a sensitivity of 0.853, a specificity of 0.815, an accuracy of 0.831 and MCC of 0.662 on the independent testing dataset. These results suggest that the proposed method can be a potential candidate for bacteriophage virion protein prediction, which may provide a useful tool to find novel antibacterial drugs and to understand the relationship between bacteriophage and host bacteria. For the convenience of the vast majority of experimental Int. J. Mol. Sci. 2015, 16 21735 scientists, a user-friendly and publicly-accessible web-server for the proposed ensemble method is established.

Summary: Conventional simultaneous localization and mapping (SLAM) has concentrated on two-dimensional (2D) map building. To adapt it to urgent search and rescue (SAR) environments, it is necessary to combine the fast and simple global 2D SLAM and three-dimensional (3D) objects of interest (OOIs) local sub-maps. The main novelty of the present work is a method for 3D OOI reconstruction based on a 2D map, thereby retaining the fast performances of the latter. A theory is established that is adapted to a SAR environment, including the object identification, exploration area coverage (AC), and loop closure detection of revisited spots. Proposed for the first is image optical flow calculation with a 2D/3D fusion method and RGB-D (red, green, blue + depth) transformation based on Joblove–Greenberg mathematics and OpenCV processing. The mathematical theories of optical flow calculation and wavelet transformation are used for the first time to solve the robotic SAR SLAM problem. The present contributions indicate two aspects: (i) mobile robots depend on planar distance estimation to build 2D maps quickly and to provide SAR exploration AC; (ii) 3D OOIs are reconstructed using the proposed innovative methods of RGB-D iterative closest points (RGB-ICPs) and 2D/3D principle of wavelet transformation. Different mobile robots are used to conduct indoor and outdoor SAR SLAM. Both the SLAM and the SAR OOIs detection are implemented by simulations and ground-truth experiments, which provide strong evidence for the proposed 2D/3D reconstruction SAR SLAM approaches adapted to post-disaster environments.

Background: Aptamer-protein interacting pairs play a variety of physiological functions and therapeutic potentials in organisms. Rapidly and effectively predicting aptamer-protein interacting pairs is significant to design aptamers binding to certain interested proteins, which will give insight into understanding mechanisms of aptamer-protein interacting pairs and developing aptamer-based therapies. Results: In this study, an ensemble method is presented to predict aptamer-protein interacting pairs with hybrid features. The features for aptamers are extracted from Pseudo K-tuple Nucleotide Composition (PseKNC) while the features for proteins incorporate Discrete Cosine Transformation (DCT), disorder information, and bi-gram Position Specific Scoring Matrix (PSSM). We investigate predictive capabilities of various feature spaces. The proposed ensemble method obtains the best performance with Youden’s Index of 0.380, using the hybrid feature space of PseKNC, DCT, bi-gram PSSM, and disorder information by 10-fold cross validation. The Relief-Incremental Feature Selection (IFS) method is adopted to obtain the optimal feature set. Based on the optimal feature set, the proposed method achieves a balanced performance with a sensitivity of 0.753 and a specificity of 0.725 on the training dataset, which indicates that this method can solve the imbalanced data problem effectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous study with a sensitivity of 0.738 and a Youden’s Index of 0.451. Conclusions: These results suggest that the proposed method can be a potential candidate for aptamer-protein interacting pair prediction, which may contribute to finding novel aptamer-protein interacting pairs and understanding the relationship between aptamers and proteins.

The Golgi Apparatus (GA) is a major collection and dispatch station for numerous proteins destined for secretion, plasma membranes and lysosomes. The dysfunction of GA proteins can result in neurodegenerative diseases. Therefore, accurate identification of protein subGolgi localizations may assist in drug development and understanding the mechanisms of the GA involved in various cellular processes. In this paper, a new computational method is proposed for identifying cis-Golgi proteins from trans-Golgi proteins. Based on the concept of Common Spatial Patterns (CSP), a novel feature extraction technique is developed to extract evolutionary information from protein sequences. To deal with the imbalanced benchmark dataset, the Synthetic Minority Over-sampling Technique (SMOTE) is adopted. A feature selection method called Random Forest-Recursive Feature Elimination (RF-RFE) is employed to search the optimal features from the CSP based features and g-gap dipeptide composition. Based on the optimal features, a Random Forest (RF) module is used to distinguish cis-Golgi proteins from trans-Golgi proteins. Through the jackknife cross-validation, the proposed method achieves a promising performance with a sensitivity of 0.889, a specificity of 0.880, an accuracy of 0.885, and a Matthew’s Correlation Coefficient (MCC) of 0.765, which remarkably outperforms previous methods. Moreover, when tested on a common independent dataset, our method also achieves a significantly improved performance. These results highlight the promising performance of the proposed method to identify Golgi-resident protein types. Furthermore, the CSP based feature extraction method may provide guidelines for protein function predictions.