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Introduction: Infections have been linked to damaged or contaminated endoscopes with visible defects. Endoscope processing standards and guidelines state endoscopes should be visually inspected every time they are used. This study evaluated a new visual inspection program using magnification and borescopes in an endoscopy department that had not previously utilized these tools., Methods: Site personnel were given visual inspection tools and training before systematically examining fully processed endoscopes twice during a 2-month period. A risk assessment protocol was used to determine whether endoscopes required recleaning, repair, or other action. Findings were documented using log sheets, photographs, and videotapes., Results: Visible damage and residue or debris were observed in 100% of 25 endoscopes at both assessments, and 76% required repair. Defects at baseline included scratches (88%); channel shredding or peeling (80%); adhesive band disintegration (80%); residual soil or debris (white 84%; black 68%; brown 40%; yellow/green 36%; and orange/red 8%); retained fluid (52%); and dents (40%). Findings were similar at follow-up., Discussion/conclusions: Visual inspection with magnification and borescopes identified actionable defects that could interfere with processing effectiveness in 100% of endoscopes. Infection preventionists have a critical role to play in supporting processing personnel now that standards, guidelines, and manufacturer instructions recommend enhanced visual inspection of every endoscope, every time., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Tumble dryer lint has been employed as a surrogate for synthetic and processed (microplastic) fibres discharged to the environment from laundering activities and exposed to marine mussels (Mytilus galloprovinciallis) in controlled experiments for a period of 7 d. A range of biological responses at different levels of organisation were subsequently determined, with copper employed concurrently as a positive control. Physiological changes were assessed from measurements of clearance rate, histopathological effects were evaluated from abnormalities in (or injuries to) gill and digestive gland tissues, and genetic damage was determined by measuring DNA strand breaks using the comet assay. With increasing lint concentration (over the range 56-180 mg L -1 ) we observed a reduction in mean clearance rate, increasing extents of abnormality in both gills (e.g. deciliation and hypertrophy) and digestive gland (e.g. atrophy and necrosis), and an increase in damage to DNA. The precise causes of these effects are unclear but likely arise from both the fibrous material itself and from chemicals (e.g. additives and metals) that are mobilised from the polymers into seawater or the digestive tract. The latter assertion is consistent with an observed increase in the release of certain trace elements (e.g. zinc) into the exposure medium with increasing lint concentration. Although microfibre concentrations we employed are significantly greater than those typically encountered in the environment, the results indicate the potential for this type of material to exert a range of adverse effects on exposed marine animals., Competing Interests: Declaration of competing interest 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., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Jupyter Notebooks have been widely adopted by many different communities, both in science and industry. They support the creation of literate programming documents that combine code, text, and execution results with visualizations and other rich media. The self-documenting aspects and the ability to reproduce results have been touted as significant benefits of notebooks. At the same time, there has been growing criticism that the way in which notebooks are being used leads to unexpected behavior, encourages poor coding practices, and makes it hard to reproduce its results. To better understand good and bad practices used in the development of real notebooks, in prior work we studied 1.4 million notebooks from GitHub. We presented a detailed analysis of their characteristics that impact reproducibility, proposed best practices that can improve the reproducibility, and discussed open challenges that require further research and development. In this paper, we extended the analysis in four different ways to validate the hypothesis uncovered in our original study. First, we separated a group of popular notebooks to check whether notebooks that get more attention have more quality and reproducibility capabilities. Second, we sampled notebooks from the full dataset for an in-depth qualitative analysis of what constitutes the dataset and which features they have. Third, we conducted a more detailed analysis by isolating library dependencies and testing different execution orders. We report how these factors impact the reproducibility rates. Finally, we mined association rules from the notebooks. We discuss patterns we discovered, which provide additional insights into notebook reproducibility. Based on our findings and best practices we proposed, we designed Julynter, a Jupyter Lab extension that identifies potential issues in notebooks and suggests modifications that improve their reproducibility. We evaluate Julynter with a remote user experiment with the goal of assessing Julynter recommendations and usability., (© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2021.)

Cotton fibre is an important natural fibre for the textile industry. The number of fibre initials determines the lint percentage, which is an important factor for cotton fibre yield. Although fibre development has been described by transcriptomic analysis, the mechanism by which the long noncoding RNA manipulates the initiation of lint and fuzz fibres remains unknown. In this study, three lines with different lint percentages were developed by crossing Xu142 with its fibreless mutant Xu142 fl. We collected the epidermal cells from the ovules with attached fibres at 0 and 5 days post anthesis (DPA) from Xu142, the fibreless mutant Xu142 fl and the three lint percent diversified lines for deep transcriptome sequencing. A total of 2641 novel genes, 35 802 long noncoding RNAs (lncRNAs) and 2262 circular RNAs (circRNAs) were identified, of which 645 lncRNAs were preferentially expressed in the fibreless mutant Xu142 fl and 651 lncRNAs were preferentially expressed in the fibre-attached lines. We demonstrated the functional roles of the three lncRNAs in fibre development via a virus-induced gene silencing (VIGS) system. Our results showed that silencing XLOC_545639 and XLOC_039050 in Xu142 fl increased the number of fibre initials on the ovules, but silencing XLOC_079089 in Xu142 resulted in a short fibre phenotype. This study established the transcriptomic repertoires in cotton fibre initiation and provided evidence for the potential functions of lncRNAs in fibre development., (© 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Jasmonic acid (JA) signaling has been well studied in Arabidopsis. Most reports focus on the role of JA in biological pathways, such as stress resistance, trichome initiation and anthocyanin accumulation. The JASMONATE ZIM-DOMAIN (JAZ) protein is one of the important repressors in the JA signaling pathway. Previous studies showed that JA functions in fiber initiation and elongation, but little is known about how JAZ genes function in fiber development. In this study, a cotton JAZ protein (GhJAZ2) containing a highly conserved TIFY motif and a C-terminal Jas domain was identified, and its function during cotton fiber development was analysed. Gene expression analysis showed that GhJAZ2 was preferentially expressed in the root, hypocotyl, flower and ovule 1 day before anthesis. Overexpression of GhJAZ2 inhibited both lint and fuzz fiber initiation, and reduced the fiber length. Yeast two-hybrid assays showed that GhJAZ2 interacted with the R2R3-MYB transcription factors GhMYB25-like and GhGL1, the bHLH transcription factor GhMYC2, the WD repeat protein GhWD40 and the unknown protein GhJI1. Among these transcription factors, previous studies showed that downregulation of GhMYB25-like leads to a fiberless phenotype in cotton seeds. Molecular and genetic evidence showed that the GhJAZ2 protein suppresses fiber initiation in the overexpressing lines by interacting with GhMYB25-like and suppressing GhMYB25-like activity. Our results suggested that GhJAZ2 functions as a primary transcription repressor during lint and fuzz fiber initiation by interacting with GhMYB25-like, GhGL1, GhMYC2, GhWD40 and GhJI1 to regulate the JA signaling pathway., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

The highly elongated single-celled cotton fibre consists of lint and fuzz, similar to the Arabidopsis trichome. Endoreduplication is an important determinant in Arabidopsis trichome initiation and morphogenesis. Fibre development is also controlled by functional homologues of Arabidopsis trichome patterning genes, although fibre cells do not have a branched shape like trichomes. The identification and characterization of the homologues of 10 key Arabidopsis trichome branching genes in Gossypium arboreum are reported here. Nuclear ploidy of fibres was determined, and gene function in cotton callus and fibre cells was investigated. The results revealed that the nuclear DNA content was constant in fuzz, whereas a limited and reversible change occurred in lint after initiation. Gossypeum arboreum branchless trichomes (GaBLT) was not transcribed in fibres. The homologue of STICHEL (STI), which is essential for trichome branching, was a pseudogene in Gossypium. Targeted expression of GaBLT, Arabidopsis STI, and the cytokinesis-repressing GaSIAMESE in G. hirsutum fibre cells cultured in vitro resulted in branching. The findings suggest that the distinctive developmental mechanism of cotton fibres does not depend on endoreduplication. This important component may be a relic function that can be activated in fibre cells.

An explanation for randomly occurring spikes on microplates in fluorescence-based assays employing shorter-wavelength readouts is presented. It is demonstrated that lint originating from standard (white cotton) lab coats is most likely to be responsible for such artifacts in assays applying wavelengths at 380 nm excitation and 450 nm emission. The fluorescence properties of this lint are discussed and compared with those of optical brighteners. An alternative to the use of cotton-based lab coats is presented, which led to a reduction of spikes in a high-throughput screening campaign by 90%.