R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.

Real-Time Closed-Loop Detection Method of vSLAM Based on a Dynamic Siamese Network

As visual simultaneous localization and mapping (vSLAM) is easy disturbed by the changes of camera viewpoint and scene appearance when building a globally consistent map, the robustness and real-time performance of key frame image selections cannot meet the requirements. To solve this problem, a real-time closed-loop detection method based on a dynamic Siamese networks is proposed in this paper. First, a dynamic Siamese network-based fast conversion learning model is constructed to handle the impact of external changes on key frame judgments, and an elementwise convergence strategy is adopted to ensure the accurate positioning of key frames in the closed-loop judgment process. Second, a joint training strategy is designed to ensure the model parameters can be learned offline in parallel from tagged video sequences, which can effectively improve the speed of closed-loop detection. Finally, the proposed method is applied experimentally to three typical closed-loop detection scenario datasets and the experimental results demonstrate the effectiveness and robustness of the proposed method under the interference of complex scenes.

An Enhanced Pedestrian Visual-Inertial SLAM System Aided with Vanishing Point in Indoor Environments

The visual-inertial simultaneous localization and mapping (SLAM) is a feasible indoor positioning system that combines the visual SLAM with inertial navigation. There are accumulated drift errors in inertial navigation due to the state propagation and the bias of the inertial measurement unit (IMU) sensor. The visual-inertial SLAM can correct the drift errors via loop detection and local pose optimization. However, if the trajectory is not a closed loop, the drift error might not be significantly reduced. This paper presents a novel pedestrian dead reckoning (PDR)-aided visual-inertial SLAM, taking advantage of the enhanced vanishing point (VP) observation. The VP is integrated into the visual-inertial SLAM as an external observation without drift error to correct the system drift error. Additionally, the estimated trajectory’s scale is affected by the IMU measurement errors in visual-inertial SLAM. Pedestrian dead reckoning (PDR) velocity is employed to constrain the double integration result of acceleration measurement from the IMU. Furthermore, to enhance the proposed system’s robustness and the positioning accuracy, the local optimization based on the sliding window and the global optimization based on the segmentation window are proposed. A series of experiments are conducted using the public ADVIO dataset and a self-collected dataset to compare the proposed system with the visual-inertial SLAM. Finally, the results demonstrate that the proposed optimization method can effectively correct the accumulated drift error in the proposed visual-inertial SLAM system.

Point-Line Visual Stereo SLAM Using EDlines and PL-BoW

Visual Simultaneous Localization and Mapping (SLAM) technologies based on point features achieve high positioning accuracy and complete map construction. However, despite their time efficiency and accuracy, such SLAM systems are prone to instability and even failure in poor texture environments. In this paper, line features are integrated with point features to enhance the robustness and reliability of stereo SLAM systems in poor texture environments. Firstly, method Edge Drawing lines (EDlines) is applied to reduce the line feature detection time. Meanwhile, the proposed method improves the reliability of features by eliminating outliers of line features based on the entropy scale and geometric constraints. Furthermore, this paper proposes a novel Bags of Word (BoW) model combining the point and line features to improve the accuracy and robustness of loop detection used in SLAM. The proposed PL-BoW technique achieves this by taking into account the co-occurrence information and spatial proximity of visual words. Experiments using the KITTI and EuRoC datasets demonstrate that the proposed stereo Point and EDlines SLAM (PEL-SLAM) achieves high accuracy consistently, including in challenging environments difficult to sense accurately. The processing time of the proposed method is reduced by 9.9% and 4.5% when compared to the Point and Line SLAM (PL-SLAM) and Point and stereo Point and Line based Visual Odometry (sPLVO) methods, respectively.

Self-Optimizing Loop Sifting and Majorization for 3D Reconstruction

Visual simultaneous localization and mapping (vSLAM) and 3D reconstruction methods have gone through impressive progress. These methods are very promising for autonomous vehicle and consumer robot applications because they can map large-scale environments such as cities and indoor environments without the need for much human effort. However, when it comes to loop detection and optimization, there is still room for improvement. vSLAM systems tend to add the loops very conservatively to reduce the severe influence of the false loops. These conservative checks usually lead to correct loops rejected, thus decrease performance. In this paper, an algorithm that can sift and majorize loop detections is proposed. Our proposed algorithm can compare the usefulness and effectiveness of different loops with the dense map posterior (DMP) metric. The algorithm tests and decides the acceptance of each loop without a single user-defined threshold. Thus it is adaptive to different data conditions. The proposed method is general and agnostic to sensor type (as long as depth or LiDAR reading presents), loop detection, and optimization methods. Neither does it require a specific type of SLAM system. Thus it has great potential to be applied to various application scenarios. Experiments are conducted on public datasets. Results show that the proposed method outperforms state-of-the-art methods.