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COPLA, a taxonomic classifier of plasmids
Background
Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence.
Results
We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the
Enterobacterales
order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized.
Conclusions
COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.
Journal Article
Can AI really replace humans on PPM surveys?
Opinion: The routine of planned preventative maintenance inspections might seem to be well suited to the capabilities of artificial intelligence – but it will be hard to replicate the human touch
Journal Article
Why PPM does not get the attention it deserves
A recent questionnaire has found that, despite its importance, clients do not give planned preventative maintenance the time or money it needs to ensure they receive appropriate advice
Journal Article
Evaluation of Electrostatic Separation of Microplastics From Mineral-Rich Environmental Samples
Reliable, easy, cost-effective and reproducible ways of extracting microplastics (MP) from environmental samples remains an important requirement for MP research. In this context, electrostatic separation is a new proposition, especially for extracting MP from mineral-rich samples and large sample volumes. However, there is little research evaluating the reliability of the technique. This study has evaluated the effectiveness of the Korona-Walzen-Scheider (KWS) system; a small-scale version of larger machines designed to sort recycling materials. Recovery rates of a variety of sizes of MP, spiked in beach sediments, were found to be highly dependent on the MP size. MP ≥ 2 mm achieved 99 - 100% recovery (with the exception of fibres: ~80%), MP of 63 – 450 µm achieved ~60 – 95% recovery and MP of 20 µm achieved ~ 45% recovery. For particle-based analysis, additional density separation is still inevitable for the analysis of small MP after KWS separation and further reduces the overall recovery rates. Mass reduction rates of beach and commercial reference sand greatly differed, 93% and 17%, respectively. Mineral analysis using SEM-EDX suggested that lower reduction rates found in commercial sand was due to high presence of small ( 450 µm, electrostatic separation is a reliable and fast approach for MP extraction from the environment.
Journal Article
Prevalence of burnout among university students in low- and middle-income countries: A systematic review and meta-analysis
Burnout is common among university students and may adversely affect academic performance. Little is known about the true burden of this preventable malady among university students in low-and-middle-income countries (LMICs).
This study aimed to systematically estimate the prevalence of burnout among university students in LMICs.
We searched PubMed, Google Scholar, CINAHL, Web of Science, African Journals Online, and Embase from the inception of each database until February 2021. Original studies were included. No study design or language restrictions were applied. A random-effects meta-analysis was performed using STATA version 16.0. Heterogeneity and publication bias were assessed using Q-statistics and funnel plots, respectively.
Fifty-five unique articles, including a total of 27,940 (Female: 16,215, 58.0%) university students from 24 LMICs were included. The Maslach Burnout Inventory (MBI) was used in 43 studies (78.2%). The pooled prevalence of burnout was 12.1% (95% Confidence Interval (CI) 11.9-12.3; I2 = 99.7%, Q = 21,464.1, p = < 0.001). The pooled prevalence of emotional exhaustion (feelings of energy depletion), cynicism (negativism), and reduced professional efficacy were, 27.8% (95% CI 27.4-28.3; I2 = 98.17%. p = <0.001), 32.6 (95% CI: 32.0-33.1; I2: 99.5%; p = < 0.001), and 29.9% (95% CI: 28.8-30.9; I2: 98.1%; p = < 0.001), respectively.
Nearly one-third of university students in LMICs experience burnout. More studies are needed to understand the causes of burnout in this key population. There is a need to validate freely available tools for use in these countries.
Journal Article
Microplastic paint particle production for spiking experiments; silicone rubber as application material provide high yield with low effort
Paint particles are a highly-important but as-yet overlooked type of microplastic commonly found in coastal sediment, although research interest is growing. There is a need for paint particles as laboratory standards for spiking experiments, however, given paint is generally only available for purchase in liquid form, a new method is needed to reliable produce laboratory-grade paint particles. The main distinguishing issue with paint particle production (as opposed to other microplastic production) is the paint must be applied to a surface in layers before then being decoupled to be processed into particles. Since paints, and especially primers, are designed specifically to strongly adhere to surfaces, using the right application material is highly important. This study tests the time and material efficiency of 2 different application materials; laboratory wax film (i.e. Parafilm®) and silicone rubber sheets (i.e. silicone baking sheets). Silicone rubber was on average 36 × more time-efficient than laboratory wax and was also 8 × more material-efficient (8 × more paint particles were produce per liquid paint used). Indeed, silicone rubber provided an essentially-perfect decoupling process, as the paint could be easily peeled away in a solid and complete layer. As such, for the future production of paint particles for laboratory purposes, silicone rubber is highly recommended as an application material.
Journal Article
Why Belgian TDD is a matter of interpretation
Flemish, French or German documents, legislative variation and insurance access are issues when conducting technical due diligence in Belgium, our third article on the process in other countries explains
Journal Article
The discursive construction of mobile chronotopes in mobile-phone messaging
This article draws on data from an ethnographic project to explore the ways in which migrant micro-entrepreneurs exploit mobile messaging apps to co-construct mobile chronotopes: dynamic configurations of time and space negotiated by geographically separated participants, who draw on different contexts and frames of understanding. Analysis of mobile messages by two couples—Chinese butchers in Birmingham and Polish shop-owners in London—informed by interview and interactional data collected at work and home, suggests they discursively negotiate and exploit multiple chronotopic layers, creating complex intersections between virtual and physical spaces in everyday interactions. We focus on the role that multilingual and multimodal semiotic resources play in co-constructing mobile chronotopes. In particular, we explore critical junctures at which communicative expectations are challenged, rendering mobile chronotope negotiation visible. Our concept of the mobile chronotope has implications for both the theorisation of mobile phone communication and understanding how chronotopes function in contemporary transnational migrant discourse.
Journal Article
Reoccurring Escherichia coli O157:H7 Strain Linked to Leafy Greens–Associated Outbreaks, 2016–2019
Genomic characterization of an Escherichia coli O157:H7 strain linked to leafy greens–associated outbreaks dates its emergence to late 2015. One clade has notable accessory genomic content and a previously described mutation putatively associated with increased arsenic tolerance. This strain is a reoccurring, emerging, or persistent strain causing illness over an extended period.
Journal Article