Witney, A. | Search bioRxiv

bioRxiv2024

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling

The detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development of a number of different bioinformatic AMR prediction tools. Although many may implement similar principles, these tools differ significantly in their supported inputs, search algorithms, parameterisation, and underlying reference databases. Each of these tools generates a report of detected AMR genes or variants in a distinct, non-standard, format. This presents a huge barrier to the comparison of results and to the modularity of tools for AMR gene prediction within bioinformatic workflows. In collaboration with 17 public health laboratories across 10 countries, the Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) data structures working group has developed and piloted a standardized output specification for the bioinformatic detection of AMR from microbial genomes. In this report, we discuss hAMRonization, a python package and command-line utility, which implements PHA4GEs AMR specification to combine the outputs of disparate antimicrobial resistance gene detection tools into a single unified format. hAMRonization can be easily extended and currently supports 18 different tools (both species-agnostic and species-specific) for the detection of genes and/or variants conferring AMR. The harmonized reports are available in tabular form, JSON format or through an interactive HTML file (e.g., https://maguire-lab.github.io/assets/interactive_report_demo.html) that can be opened within the browser for navigable data exploration. As of 2024-03-07 hAMRonization has been downloaded [~]12,500 times, incorporated into >9 public bioinformatic tools and workflows, and been internally adopted by several national and international public health groups. The hAMRonization tool and underlying specification are open-source and freely available through PyPI, conda and GitHub (https://github.com/pha4ge/hAMRonization).

bioinformatics↗

bioRxiv2019

Can transcranial direct current stimulation over the dorsolateral prefrontal cortex enhance proprioception?

IntroductionProprioception (perception of ones limb position) is critical for accurate and consistent movement, and is processed by the sensorimotor cortex. Increased prefrontal activity is associated with improved proprioception and motor performance. Anodal transcranial direct current stimulation (tDCS) of the left dorsolateral prefrontal cortex (DLPFC) has been found to increase activity of the sensorimotor cortex. Thus, this study aimed to investigate whether anodal tDCS of the DLPFC may enhance proprioception measured with a target task. It was hypothesized that tDCS over the left DLPFC would improve motor performance (error and variability) on a target task completed without vision. DesignSingle blind, within-participant, sham-controlled trial. MethodsFifteen healthy young adults (M:F=6:9, age=23.3 years) completed 18 trials of a computerized target task (manipulating a mouse) with their non-dominant upper-limb, with and without vision, before and after (pre/post assessment) 20-minutes of stimulation (anodal tDCS of the left DLPFC) and sham conditions. Averages and coefficient of variation (CV, variability between trials) of spatio-temporal parameters associated with the movement were measured. Stimulation/ sham sessions were counterbalanced (stimulation first session, n=8), with each session separated by one week. Repeated-measures ANOVA and pairwise comparisons (95% confidence intervals [CI]) were conducted. ResultsRegarding distance travelled CV, a significant interaction between condition and assessment (F(1,14)=5.09, p=0.041) demonstrated that variability was significantly less post-stimulation compared to pre (p=0.003). A significant interaction between assessment and vision (F(1,14)=30.08, p<0.001) regarding distance travelled CV showed that without vision, variability was significantly less at post compared to pre (p<0.001), and this decrease was found after the stimulation condition only (95% CI = {Delta} 7.4 +/- 1.6 [4.0 to 10.9]). ConclusionSince variability of distance travelled during the target task without vision was lower post-stimulation compared to pre, consistency of movement without vision, and therefore proprioception, may have been enhanced by anodal tDCS of the DLPFC. This improvement could be due to modulation of fronto-striatal-thalamic circuits. These findings may be the first step in developing tDCS methods as an effective adjunct therapy for dysfunctional proprioception in various disorders, such as Parkinsons disease.

neuroscience↗