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The implementation of Hi-C reads in the de novo genome assembly process allows the ordering of large regions of the genome in scaffolds and the generation of chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and each tool has advantages and disadvantages that need to be carefully evaluated before their adoption. We generated two de novo assemblies of Arabidopsis thaliana obtained from the same raw PacBio HiFi and Oxford Nanopore Technologies data. We scaffolded the assemblies implementing Hi-C reads with the scaffolders 3D-DNA, SALSA2, and YaHS, with the aim of identifying the tool providing the most accurate assembly. The scaffolded assemblies were evaluated according to contiguity, completeness, accuracy, and structural correctness. In our analysis, YaHS proved to be the best-performing bioinformatics tool for scaffolding de novo genome assemblies in Arabidopsis thaliana ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Obinu, Trivedi and Porceddu.)

Background: The gut microbiota has been implicated in adult obesity, but the causality is still unclear. It has been hypothesized that an obesity-prone gut microbiota can be established in infancy, but only few studies have examined the early-life gut microbiota in relation to obesity in childhood, and no consistent associations have been reported. Here, we examine the association between the early-life gut microbiota and body mass index (BMI) development and body composition throughout childhood., Methods: Gut microbiota from stool were collected from 700 children in the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC 2010 ) cohort at ages of 1 week, 1month, 1 year, 4 years, and 6 years and analyzed by 16S rRNA gene sequencing. Outcomes included BMI World Health Organization (WHO) Z scores (zBMI), overweight (zBMI > 1.04) and obesity (zBMI > 1.64) (0-10 years), and adiposity rebound and body composition from dual-energy X-ray absorptiometry at 6 years., Findings: The early-life gut microbiota diversity, overall composition, and individual taxon abundances in unsupervised and supervised models were not consistently associated with either current or later BMI Z scores, overweight, obesity, adiposity rebound, or body composition in childhood., Conclusions: In a deeply characterized longitudinal birth cohort, we did not observe any consistent associations between the early-life gut microbiota and BMI or risk of obesity in later childhood. While this does not conclusively rule out a relationship, it suggests that if such associations exist, they may be more complex and potentially influenced by factors emerging later in life, including lifestyle changes., Funding: COPSAC is funded by private and public research funds (all listed on www.copsac.com)., Competing Interests: Declaration of interests J.T. has received a speaking fee from AstraZeneca., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: In environmental bacteria, the selective advantage of antibiotic resistance genes (ARGs) can be increased through co-localization with genes such as other ARGs, biocide resistance genes, metal resistance genes, and virulence genes (VGs). The gut microbiome of infants has been shown to contain numerous ARGs, however, co-localization related to ARGs is unknown during early life despite frequent exposures to biocides and metals from an early age., Results: We conducted a comprehensive analysis of genetic co-localization of resistance genes in a cohort of 662 Danish children and examined the association between such co-localization and environmental factors as well as gut microbial maturation. Our study showed that co-localization of ARGs with other resistance and virulence genes is common in the early gut microbiome and is associated with gut bacteria that are indicative of low maturity. Statistical models showed that co-localization occurred mainly in the phylum Proteobacteria independent of high ARG content and contig length. We evaluated the stochasticity of co-localization occurrence using enrichment scores. The most common forms of co-localization involved tetracycline and fluoroquinolone resistance genes, and, on plasmids, co-localization predominantly occurred in the form of class 1 integrons. Antibiotic use caused a short-term increase in mobile ARGs, while non-mobile ARGs showed no significant change. Finally, we found that a high abundance of VGs was associated with low gut microbial maturity and that VGs showed even higher potential for mobility than ARGs., Conclusions: We found that the phenomenon of co-localization between ARGs and other resistance and VGs was prevalent in the gut at the beginning of life. It reveals the diversity that sustains antibiotic resistance and therefore indirectly emphasizes the need to apply caution in the use of antimicrobial agents in clinical practice, animal husbandry, and daily life to mitigate the escalation of resistance. Video Abstract., (© 2024. The Author(s).)

This article discusses the significance of knee joint mechanics and the consequences of knee dysfunctions on an individual's quality of life. The utilization of active knee braces, which incorporate concepts of mechatronics systems, is investigated here as a potential treatment option. The complexity of the construction of the knee joint, which has six degrees of motion and is more prone to injury since it bears weight, is emphasized in this article. By wearing braces and using other support devices, one's knee can increase stability and mobility. In addition, the paper discusses various technologies that can be used to measure the knee adduction moment and supply spatial information on gait. Actuators for active knee braces must be compact, lightweight, and capable of producing a significant amount of torque; as a result, electric, hydraulic, and pneumatic actuators are the most common types. Creating control mechanisms, such as position control techniques and force/torque control approaches, is essential to knee exoskeleton research and development. These methods might make knee joint rehabilitation and assistive technology safer and more effective., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)