Sea stack plots: Replacing bar charts with histograms

Graphs in research articles can increase the comprehension of statistical data but may mislead readers if poorly designed. We propose a new plot type, the sea stack plot, which combines vertical histograms and summary statistics to represent large univariate datasets accurately, usefully, and efficiently. We compare five commonly used plot types (dot and whisker plots, boxplots, density plots, univariate scatter plots, and dot plots) to assess their relative strengths and weaknesses when representing distributions of data commonly observed in biological studies. We find the assessed plot types are either difficult to read at large sample sizes or have the potential to misrepresent certain distributions of data, showing the need for an improved method of data visualisation. We present an analysis of the plot types used in four ecology and conservation journals covering multiple areas of these research fields, finding widespread use of uninformative bar charts and dot and whisker plots (60% of all panels showing univariate data from multiple groups for the purpose of comparison). Some articles presented more informative figures by combining plot types (16% of panels), generally boxplots and a second layer such as a flat density plot, to better display the data. This shows an appetite for more effective plot types within conservation and ecology, which may further increase if accurate and user-friendly plot types were made available. Finally, we describe sea stack plots and explain how they overcome the weaknesses associated with other alternatives to uninformative plots when used for large and/or unevenly distributed data. We provide a tool to create sea stack plots with our R package 'seastackplot', available through GitHub.

An ethnographic study evaluating emergency obstetric care education and training in a remote, fragile region of Southeast Asia: Study protocol

AIM

To evaluate emergency obstetric care education and training within a medical assistant training program, being delivered in a remote, fragile region of Southeast Asia. This will aid in the identification of potential areas of enhancement to improve the management of obstetric emergencies.

DESIGN

An ethnographic study, adopting a multi-methods approach.

METHODS

Emergency obstetric care education and training will be assessed through documentary analysis and interviews (online or face-to-face) with educators and trainers (N ~ 6-7). Student experiences will be explored using in-person focus groups, facilitated by an external trainer involved in delivering the program (N ~ 10-12). A reflective field diary will provide insight into the lived experience of postgraduate students (N ~ 4-5). Data will be collected between May 2022 and May 2023. The full data set will be triangulated and analysed using the READ approach; (1) ready your materials, (2) extract data, (3) analyse data and (4) distil your findings. Institutional ethical approval was obtained from a university in October 2021, and inter-country regional access was gained following adherence to their local ethical requirements.

IMPLICATIONS FOR THE PROFESSION AND PATIENT CARE

The findings from this study may help to inform the future design of the medical assistant training program. It is anticipated that the knowledge gained from this study will enhance the education and training of mid-level health providers at local, national, and international levels. This work intends to contribute to addressing Sustainable Development Goal 3, Target 1 of reducing maternal mortality to 70:100,000 live births in low-income countries.

REPORTING METHOD

This protocol adhered to the Standards for Reporting Qualitative Research (SRQR) checklist.

PATIENT OR PUBLIC CONTRIBUTION

No formal PPI has been undertaken; however, stakeholders involved in delivering the education and training have been consulted.

Using in vitro bioassays to guide the development of safer bio-based polymers for use in food packaging

Petroleum-based polymers traditionally used for plastic packaging production have been shown to leach dangerous chemicals such as bisphenol-A (BPA). Bio-based polymers are potentially safer alternatives, and many can be sustainably sourced from waste streams in the food industry. This study assesses bio-based polymers undergoing food packaging development for migration of endocrine disrupting leachates at the level of estrogen, androgen and progestagen nuclear receptor transcriptional activity. Reporter gene assays were coupled with migration testing, performed using standardised test conditions for storage and temperature. Test samples include nine bio-based polymers and four inorganic waste additives mixed with a traditional petroleum-based polymer, polypropylene. Thermoplastic starch material, polybutylene succinate, polycaprolactone, polybutylene adipate terephthalate (PBAT), two polylactic acid (PLA)/PBAT blends, polyhydroxybutyrate (PHB) and eggshell/polypropylene (10:90) presented no significant reduction in metabolic activity or hormonal activity under any test condition. Polypropylene (PP) presented no hormonal activity. Metabolic activity was reduced in the estrogen responsive cell line after 10 days migration testing of eggshell/polypropylene (0.1:99.9) in MeOH at 40°C, and PP in MeOH and dH₂0. Estrogenic agonist activity was observed after 10 days in poultry litter ash/polypropylene (10:90) in MeOH at 20°C and 40°C, poultry feather based polymer in MeOH and dH₂O at 40°C, and eggshell/polypropylene (40:60) and PLA in dH₂O at 40°C. Activity was within a range of 0.26–0.50 ng 17β-estradiol equivalents per ml, equating to an estrogenic potency of 3–∼2800 times less than the estrogenic leachate BPA. Poultry litter ash/polypropylene (10:90) in MeOH for 10 days presented estrogenic activity at 20°C and 40°C within the above range and anti-androgenic activity at 40°C. Progestagenic activity was not observed for any of the compounds under any test condition. Interestingly, lower concentrations of eggshell or PP may eliminate eggshell estrogenicity and PP toxicity. Alternatively eggshell may bind and eliminate the toxic elements of PP. Similarly, PLA estrogenic activity was removed in both PLA/PBAT blends. This study demonstrates the benefits of bioassay guidance in the development of safer and sustainable packaging alternatives to petroleum-based plastics. Manipulating the types of additives and their formulations alongside toxicological testing may further improve safety aspects.

Developmental Regulation and Functional Prediction of microRNAs in an Expanded Fasciola hepatica miRNome

The liver fluke, Fasciola hepatica, is a global burden on the wellbeing and productivity of farmed ruminants, and a zoonotic threat to human health. Despite the clear need for accelerated discovery of new drug and vaccine treatments for this pathogen, we still have a relatively limited understanding of liver fluke biology and host interactions. Noncoding RNAs, including micro (mi)RNAs, are key to transcriptional regulation in all eukaryotes, such that an understanding of miRNA biology can shed light on organismal function at a systems level. Four previous publications have reported up to 89 mature miRNA sequences from F. hepatica, but our data show that this does not represent a full account of this species miRNome. We have expanded on previous studies by sequencing, for the first time, miRNAs from multiple life stages (adult, newly excysted juvenile (NEJ), metacercariae and adult-derived extracellular vesicles (EVs)). These experiments detected an additional 61 high-confidence miRNAs, most of which have not been described in any other species, expanding the F. hepatica miRNome to 150 mature sequences. We used quantitative (q)PCR assays to provide the first developmental profile of miRNA expression across metacercariae, NEJ, adult and adult-derived Evs. The majority of miRNAs were expressed most highly in metacercariae, with at least six distinct expression clusters apparent across life stages. Intracellular miRNAs were functionally analyzed to identify target mRNAs with inversely correlated expression in F. hepatica tissue transcriptomes, highlighting regulatory interactions with key virulence transcripts including cathepsin proteases, and neuromuscular genes that control parasite growth, development and motility. We also linked 28 adult-derived EV miRNAs with downregulation of 397 host genes in F. hepatica-infected transcriptomes from ruminant lymph node, peripheral blood mononuclear cell (PBMC) and liver tissue transcriptomes. These included genes involved in signal transduction, immune and metabolic pathways, adding to the evidence for miRNA-based immunosuppression during fasciolosis. These data expand our understanding of the F. hepatica miRNome, provide the first data on developmental miRNA regulation in this species, and provide a set of testable hypotheses for functional genomics interrogations of liver fluke miRNA biology.