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Background Bacteria of the Borrelia burgdorferi sensu lato (s.l.) complex can cause Lyme borreliosis. Different B. burgdorferi s.l. genospecies vary in their host and vector associations and human pathogenicity but the genetic basis for these adaptations is unresolved and requires completed and reliable genomes for comparative analyses. The de novo assembly of a complete Borrelia genome is challenging due to the high levels of complexity, represented by a high number of circular and linear plasmids that are dynamic, showing mosaic structure and sequence homology. Previous work demonstrated that even advanced approaches, such as a combination of short-read and long-read data, might lead to incomplete plasmid reconstruction. Here, using recently developed high-fidelity (HiFi) PacBio sequencing, we explored strategies to obtain gap-free, complete and high quality Borrelia genome assemblies. Optimizing genome assembly, quality control and refinement steps, we critically appraised existing techniques to create a workflow that lead to improved genome reconstruction. Results Despite the latest available technologies, stand-alone sequencing and assembly methods are insufficient for the generation of complete and high quality Borrelia genome assemblies. We developed a workflow pipeline for the de novo genome assembly for Borrelia using several types of sequence data and incorporating multiple assemblers to recover the complete genome including both circular and linear plasmid sequences. Conclusion Our study demonstrates that, with HiFi data and an ensemble reconstruction pipeline with refinement steps, chromosomal and plasmid sequences can be fully resolved, even for complex genomes such as Borrelia . The presented pipeline may be of interest for the assembly of further complex microbial genomes.

RGGB sensor arrays are commonly used in digital cameras and mobile photography. However, images of extreme dark-light conditions often suffer from insufficient exposure because the sensor receives insufficient light. The existing methods mainly employ U-Net variants, multi-stage camera parameter simulation, or image parameter processing to address this issue. However, those methods usually apply color adjustments evenly across the entire image, which may cause extensive blue or green noise artifacts, especially in images with dark backgrounds. This study attacks the problem by proposing a novel multi-step process for image enhancement. The pipeline starts with a self-attention U-Net for initial color restoration and applies a Color Correction Matrix (CCM). Thereafter, High Dynamic Range (HDR) image reconstruction techniques are utilized to improve exposure using various Camera Response Functions (CRFs). After removing under- and over-exposed frames, pseudo-HDR images are created through multi-frame fusion. Also, a comparative analysis is conducted based on a standard dataset, and the results show that the proposed approach performs better in creating well-exposed images and improves the Peak-Signal-to-Noise Ratio (PSNR) by 0.16 dB compared to the benchmark methods.

Mesh simplification is an effective way to solve the contradiction between 3D models and limited transmission bandwidth and smooth model rendering. The existing mesh simplification algorithms usually have problems of texture distortion, deformation of different degrees, and no texture simplification. In this paper, a model simplification algorithm suitable for 3D reconstruction is proposed by taking full advantage of the recovered 3D scene structure and calibrated images. First, the reference 3D model scene is constructed on the basis of the original mesh; second, the images are collected on the basis of the reference 3D model scene; then, the mesh and texture are simplified by using the reference image set combined with the QEM algorithm. Lastly, the 3D model data of a town in Tengzhou are used for experimental verification. The results show that the algorithm proposed in this paper basically has no texture distortion and deformation problems in texture simplification and can effectively reduce the amount of texture data, with good feasibility.

Ground-penetrating radar (GPR) plays a critical role in detecting underground targets, particularly locating and characterizing leaks in buried pipelines. However, the complex nature of GPR images related to pipeline leaks, combined with the limitations of existing neural network-based inversion methods, such as insufficient feature extraction and low inversion accuracy, poses significant challenges for effective leakage reconstruction. To address these challenges, this paper proposes an enhanced UNet++-based model: the Multi-Scale Directional Network PlusPlus (MSDNet++). The network employs an encoder–decoder architecture, in which the encoder incorporates multi-scale directional convolutions with coordinate attention to extract and compress features across different scales effectively. The decoder fuses multi-level features through dense skip connections and further enhances the representation of critical information via coordinate attention, enabling the accurate inversion of dielectric constant images. Experimental results on both simulated and real-world data demonstrate that MSDNet++ can accurately invert the location and extent of buried pipeline leaks from GPR B-scan images.

Doc number: O42

The Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity.

Mapping the environment of a vehicle and localizing a vehicle within that unknown environment are complex issues. Although many approaches based on various types of sensory inputs and computational concepts have been successfully utilized for ground robot localization, there is difficulty in localizing an unmanned aerial vehicle (UAV) due to variation in altitude and motion dynamics. This paper proposes a robust and efficient indoor mapping and localization solution for a UAV integrated with low-cost Light Detection and Ranging (LiDAR) and Inertial Measurement Unit (IMU) sensors. Considering the advantage of the typical geometric structure of indoor environments, the planar position of UAVs can be efficiently calculated from a point-to-point scan matching algorithm using measurements from a horizontally scanning primary LiDAR. The altitude of the UAV with respect to the floor can be estimated accurately using a vertically scanning secondary LiDAR scanner, which is mounted orthogonally to the primary LiDAR. Furthermore, a Kalman filter is used to derive the 3D position by fusing primary and secondary LiDAR data. Additionally, this work presents a novel method for its application in the real-time classification of a pipeline in an indoor map by integrating the proposed navigation approach. Classification of the pipeline is based on the pipe radius estimation considering the region of interest (ROI) and the typical angle. The ROI is selected by finding the nearest neighbors of the selected seed point in the pipeline point cloud, and the typical angle is estimated with the directional histogram. Experimental results are provided to determine the feasibility of the proposed navigation system and its integration with real-time application in industrial plant engineering.

Background Constraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The starting point and cornerstone of all such modeling is a genome-scale metabolic network reconstruction. The creation, further development, and application of such networks is a growing field of research thanks to a plethora of readily accessible computational tools. While the majority of studies are focused on single-species analyses, typically of a microbe, the computational study of communities of organisms is gaining attention. Similarly, reconstructions that are unified for a multi-cellular organism have gained in popularity. Consequently, the rapid generation of genome-scale metabolic reconstructed networks is crucial. While multiple web-based or stand-alone tools are available for automated network reconstruction, there is, however, currently no publicly available tool that allows the swift assembly of draft reconstructions of community metabolic networks and consolidated metabolic networks for a specified list of organisms. Results Here, we present AutoKEGGRec, an automated tool that creates first draft metabolic network reconstructions of single organisms, community reconstructions based on a list of organisms, and finally a consolidated reconstruction for a list of organisms or strains. AutoKEGGRec is developed in Matlab and works seamlessly with the COBRA Toolbox v3, and it is based on only using the KEGG database as external input. The generated first draft reconstructions are stored in SBML files and consist of all reactions for a KEGG organism ID and corresponding linked genes. This provides a comprehensive starting point for further refinement and curation using the host of COBRA toolbox functions or other preferred tools. Through the data structures created, the tool also facilitates a comparative analysis of metabolic content in any given number of organisms present in the KEGG database. Conclusion AutoKEGGRec provides a first step in a metabolic network reconstruction process, filling a gap for tools creating community and consolidated metabolic networks. Based only on KEGG data as external input, the generated reconstructions consist of data with a directly traceable foundation and pedigree. With AutoKEGGRec, this kind of modeling is made accessible to a wider part of the genome-scale metabolic analysis community.

By applying vision sensing to realize online intelligent control on the pipeline welding process, the welding efficiency and qualification rate of pipeline girth butt joint during on-site construction of long-distance oil and gas pipelines can be effectively improved. During the pipeline external welding process, based on the designed combined line structured lights vision sensor (C-LSLVS), a partitioned time–frequency-space (PTFS) image processing algorithm is proposed to extract the laser centerline for the deformed laser lines image of double-V composite groove. The algorithm first utilizes information in the time domain to remove random interference from the image, and then, based on Radon transform (RT) and discrete Fourier transform (DFT), other stationary interferences can be eliminated and laser line characteristics can be enhanced by back-projection reconstruction in the frequency domain and space domain, so the stable and accurate extraction of laser centerline can be achieved under different situations. Subsequently, the theoretical analysis and error calculation of the pipeline groove sizes and related parameters solution model based on the local plane fitting method are carried out, and high-precision calculations of the parameters are completed. Finally, an intelligent pipeline welding system based on the C-LSLVS is constructed. In the intelligent welding experiment, the maximum detection error of the pipeline welding groove sizes did not exceed 0.20 mm, and the weld seam tracking deviation did not exceed 0.25 mm. The welding results show that the system has important application value for the development of pipeline intelligent welding.