Recommendations for accelerating open preprint peer review to improve the culture of science

Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.

Europe PMC in 2023

Europe PMC (https://europepmc.org/) is an open access database of life science journal articles and preprints, which contains over 42 million abstracts and over 9 million full text articles accessible via the website, APIs and bulk download. This publication outlines new developments to the Europe PMC platform since the last database update in 2020 (1) and focuses on five main areas. (i) Improving discoverability, reproducibility and trust in preprints by indexing new preprint content, enriching preprint metadata and identifying withdrawn and removed preprints. (ii) Enhancing support for text and data mining by expanding the types of annotations provided and developing the Europe PMC Annotations Corpus, which can be used to train machine learning models to increase their accuracy and precision. (iii) Developing the Article Status Monitor tool and email alerts, to notify users about new articles and updates to existing records. (iv) Positioning Europe PMC as an open scholarly infrastructure through increasing the portion of open source core software, improving sustainability and accessibility of the service.

Can we evidence-base injury prevention and management in women's football? A scoping review

This review aimed, as part of a larger FIFA project aiming to steer women's football research, to scope literature on any level of competitive football for women, to understand the current quantity of research on women's football injuries. The study reviewed all injury-related papers scoped by a recent scoping review mapping all published women's football research with an updated search performed on 23 February 2021. Eligibility criteria assessment followed the recent scoping review with injury-specific research focus. A total of 497 studies were scoped. Most studies contained an epidemiological (N = 226; 45%) or risk factors assessment (N = 105; 21%). Less assessed areas included financial burden (N = 1; <1%) and injury awareness (N = 5; 1%). 159 studies (32%) assessed injuries of the whole body. The most common single location assessed in the literature was the knee (N = 134, 27%), followed by head/face (N =108, 22%). These numbers were, however, substantially lowered, when subdivided by playing level and age-group. The volume of research focuses especially on descriptive research and specific body locations (head/face and knee). Although information can be taken from studies in other sports, more football-specific studies to support management and prevention of injuries are warranted.

Searching and Evaluating Publications and Preprints Using Europe PMC

In the field of life sciences there is a growing need for literature analysis tools that help scientists tackle information overload. Europe PubMed Central (Europe PMC), a partner of PubMed Central (PMC; National Library of Medicine, 2022), is an open access database of over 41 million life science publications and preprints, enriched with supporting data, reviews, protocols, and other relevant resources. Europe PMC is a trusted repository of choice for many life science funders (Europe PMC, 2022a), offering a suite of innovative search tools that allow users to search and evaluate the literature, including finding highly cited articles, preprints with community peer reviews, or papers referencing a proteomics dataset in the figure legend. In addition, Europe PMC utilizes text-mining to help researchers identify key terms and find data and evidence in the literature. First-time users often do not utilize the wealth of tools Europe PMC offers and can feel overwhelmed about how to perform the most effective search. This protocol, describing how to search and evaluate publications and preprints using Europe PMC, demonstrates how to carry out more efficient and effective literature searches using the tools provided by Europe PMC. This includes discovering the latest findings on a research topic, following research from a specific author, journal, or preprint server, exploring literature on a new method, expanding your reading list with relevant articles, as well as accessing and evaluating publications and preprints of interest. © 2023 EMBL-EBI. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Finding articles and preprints on a topic of interest Basic Protocol 2: Accessing an article Basic Protocol 3: Browsing the article Basic Protocol 4: Evaluating the article Basic Protocol 5: Refining search results Basic Protocol 6: Finding research by author Basic Protocol 7: Finding a specific article Basic Protocol 8: Finding information about a methodology Basic Protocol 9: Finding evidence of biological interactions, relations, and modifications Basic Protocol 10: Finding data behind a publication Basic Protocol 11: Expanding a reading list and building a bibliography Basic Protocol 12: Staying on top of the current literature.

EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises the status of services that EMBL-EBI data resources provide to scientific communities globally. The scale, openness, rich metadata and extensive curation of EMBL-EBI added-value databases makes them particularly well-suited as training sets for deep learning, machine learning and artificial intelligence applications, a selection of which are described here. The data resources at EMBL-EBI can catalyse such developments because they offer sustainable, high-quality data, collected in some cases over decades and made openly availability to any researcher, globally. Our aim is for EMBL-EBI data resources to keep providing the foundations for tools and research insights that transform fields across the life sciences.

Premature translation of the Drosophila zygotic genome activator Zelda is not sufficient to precociously activate gene expression

Following fertilization, the unified germ cells rapidly transition to a totipotent embryo. Maternally deposited mRNAs encode the proteins necessary for this reprogramming as the zygotic genome remains transcriptionally quiescent during the initial stages of development. The transcription factors required to activate the zygotic genome are among these maternally deposited mRNAs and are robustly translated following fertilization. In Drosophila, the mRNA encoding Zelda, the major activator of the zygotic genome, is not translated until 1 h after fertilization. Here we demonstrate that zelda translation is repressed in the early embryo by the TRIM-NHL protein Brain tumor (BRAT). BRAT also regulates Zelda levels in the larval neuroblast lineage. In the embryo, BRAT-mediated translational repression is regulated by the Pan Gu kinase, which is triggered by egg activation. The Pan Gu kinase phosphorylates translational regulators, suggesting that Pan Gu kinase activity alleviates translational repression of zelda by BRAT and coupling translation of zelda with that of other regulators of early embryonic development. Using the premature translation of zelda in embryos lacking BRAT activity, we showed that early translation of a zygotic genome activator is not sufficient to drive precocious gene expression. Instead, Zelda-target genes showed increased expression at the time they are normally activated. We propose that transition through early development requires the integration of multiple processes, including the slowing of the nuclear division cycle and activation of the zygotic genome. These processes are coordinately controlled by Pan Gu kinase-mediated regulation of translation.

Tethering gene regulation to chromatin organization

[Figure: see text].

Compact X-Band Electron Linac for Radiotherapy and Security Applications

RadiaBeam has developed a 6 MeV accelerator that is compact and light enough to be placed on a robotic arm or light truck. The main drivers of size and weight in conventional accelerators are the power source and the shielding. Small dimensions are enabled by operation at 9.3 GHz frequency (X-band), which allows reducing the size and weight of all accelerator components. Thanks to the robust design of the accelerating structure, the accelerator can be used as a source for novel cargo inspection and radiotherapy techniques. In this paper, we present the linac design and its components, as well the results of the experimental demonstration of beam acceleration.

Intensity-modulated Radiotherapy for Rectal Cancer in the UK in 2020

AIMS

Preoperative (chemo)radiotherapy followed by total mesorectal excision is the current standard of care for patients with locally advanced rectal cancer. The use of intensity-modulated radiotherapy (IMRT) for rectal cancer is increasing in the UK. However, the extent of IMRT implementation and current practice was not previously known. A national survey was commissioned to investigate the landscape of IMRT use for rectal cancer and to inform the development of national rectal cancer IMRT guidance.

MATERIALS AND METHODS

A web-based survey was developed by the National Rectal Cancer IMRT Guidance working group in collaboration with the Royal College of Radiologists and disseminated to all UK radiotherapy centres. The survey enquired about the implementation of IMRT with a focus on the following aspects of the workflow: dose fractionation schedules and use of a boost; pre-treatment preparation and simulation; target volume/organ at risk definition; treatment planning and treatment verification. A descriptive statistical analysis was carried out.

RESULTS

In total, 44 of 63 centres (70%) responded to the survey; 30/44 (68%) and 36/44 (82%) centres currently use IMRT to treat all patients and selected patients with rectal cancer, respectively. There was general agreement concerning several aspects of the IMRT workflow, including patient positioning, use of intravenous contrast and bladder protocols. Greater variation in practice was identified regarding rectal protocols; use of a boost to primary/nodal disease; target volume delineation; organ at risk delineation and dose constraints and treatment verification. Delineation of individual small bowel loops and daily volumetric treatment verification were considered potentially feasible by most centres.

CONCLUSION

This survey identified that IMRT is already used to treat rectal cancer in many UK radiotherapy centres, but there is heterogeneity between centres in its implementation and practice. These results have been a valuable aid in framing the recommendations within the new National Rectal Cancer IMRT Guidance.

Diagnosis of normal chest radiographs using an autonomous deep-learning algorithm

AIM

To evaluate the suitability of a deep-learning (DL) algorithm for identifying normality as a rule-out test for fully automated diagnosis in frontal adult chest radiographs (CXR) in an active clinical pathway.

MATERIALS AND METHODS

This multicentre study included 3,887 CXRs from four distinct NHS institutions. A convolutional neural network (CNN) was developed and trained prior to this study and was used to classify a subset of examinations with the lowest abnormality scores as high confidence normal (HCN). For each radiograph, the ground truth (GT) was established using two independent reviewers and an arbitrator in case of discrepancy.

RESULTS

The DL algorithm was able to classify 15% of all examinations as HCN, with a corresponding precision of 97.7%. There were 0.33% of examinations classified incorrectly as HCN, with 84.6% of these examinations identified as borderline cases by the radiologist GT process.

CONCLUSION

A DL algorithm can achieve a high level of precision as a fully automated diagnostic tool for reporting a subset of CXRs as normal. The removal of 15% of all CXRs has the potential to significantly reduce workload and focus radiology resources on more complex examinations. To optimise performance, site-specific deployment of algorithms should occur with robust feedback mechanisms for incorrect classifications.

Spontaneous Escherichia coli Meningitis and Pyogenic Ventriculitis in an Adult Receiving Anti-Tumour Necrosis Factor Alpha Therapy

Presentation A 60-year-old male taking etanercept for ankylosing spondylitis was admitted to hospital with confusion and reduced level of consciousness over the preceding 24 hours. Diagnosis Magnetic Resonance Imaging (MRI) of his brain revealed pyogenic ventriculitis, and Escherichia coli was cultured from CSF. Treatment He required placement of an external ventricular drain and was treated with a prolonged course of intravenous ceftriaxone. Conclusion To our knowledge, this is the first reported case of spontaneous Gram-negative bacillary meningitis in a patient on anti-tumour necrosis factor (TNF)-alpha therapy, highlighting the risk of rare but serious infections associated with this class of medication.

Longitudinal characterisation of haematological and biochemical parameters in cancer patients prior to and during COVID-19 reveals features associated with outcome

BACKGROUND

Cancer patients are at increased risk of death from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Cancer and its treatment affect many haematological and biochemical parameters, therefore we analysed these prior to and during coronavirus disease 2019 (COVID-19) and correlated them with outcome.

PATIENTS AND METHODS

Consecutive patients with cancer testing positive for SARS-CoV-2 in centres throughout the United Kingdom were identified and entered into a database following local governance approval. Clinical and longitudinal laboratory data were extracted from patient records. Data were analysed using Mann-Whitney U test, Fisher's exact test, Wilcoxon signed rank test, logistic regression, or linear regression for outcomes. Hierarchical clustering of heatmaps was performed using Ward's method.

RESULTS

In total, 302 patients were included in three cohorts: Manchester (n = 67), Liverpool (n = 62), and UK (n = 173). In the entire cohort (N = 302), median age was 69 (range 19-93 years), including 163 males and 139 females; of these, 216 were diagnosed with a solid tumour and 86 with a haematological cancer. Preinfection lymphopaenia, neutropaenia and lactate dehydrogenase (LDH) were not associated with oxygen requirement (O2) or death. Lymphocyte count (P < 0.001), platelet count (P = 0.03), LDH (P < 0.0001) and albumin (P < 0.0001) significantly changed from preinfection to during infection. High rather than low neutrophils at day 0 (P = 0.007), higher maximal neutrophils during COVID-19 (P = 0.026) and higher neutrophil-to-lymphocyte ratio (NLR; P = 0.01) were associated with death. In multivariable analysis, age (P = 0.002), haematological cancer (P = 0.034), C-reactive protein (P = 0.004), NLR (P = 0.036) and albumin (P = 0.02) at day 0 were significant predictors of death. In the Manchester/Liverpool cohort 30 patients have restarted therapy following COVID-19, with no additional complications requiring readmission.

CONCLUSION

Preinfection biochemical/haematological parameters were not associated with worse outcome in cancer patients. Restarting treatment following COVID-19 was not associated with additional complications. Neutropaenia due to cancer/treatment is not associated with COVID-19 mortality. Cancer therapy, particularly in patients with solid tumours, need not be delayed or omitted due to concerns that treatment itself increases COVID-19 severity.

Recognizing the value of software: a software citation guide

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

Recognizing the value of software: a software citation guide

Software is as integral as a research paper, monograph, or dataset in terms of facilitating the full understanding and dissemination of research. This article provides broadly applicable guidance on software citation for the communities and institutions publishing academic journals and conference proceedings. We expect those communities and institutions to produce versions of this document with software examples and citation styles that are appropriate for their intended audience. This article (and those community-specific versions) are aimed at authors citing software, including software developed by the authors or by others. We also include brief instructions on how software can be made citable, directing readers to more comprehensive guidance published elsewhere. The guidance presented in this article helps to support proper attribution and credit, reproducibility, collaboration and reuse, and encourages building on the work of others to further research.

Long-term biological variability and the generation of a new reference interval for plasma N-terminal pro-B-type natriuretic peptide in Labrador retrievers

OBJECTIVES

First, to investigate the biological variability of N-terminal pro-B-type natriuretic peptide (NT-proBNP) in healthy Labrador retrievers and compare this with current laboratory recommendations for dilated cardiomyopathy screening. Second, to calculate a breed-specific reference interval and validate it in a retrospective cohort.

MATERIALS AND METHODS

Plasma NT-proBNP was measured in 51 clinically healthy Labrador retrievers at 0, 2, 4, 6 and 8 weeks. Coefficient of variation for individual dogs over time, the coefficient of variation for the group at each time point and the index of individuality were calculated. A reference interval was derived and tested on a clinical dataset available from four UK cardiology referral centres.

RESULTS

Median NT-proBNP was 865 pmol/L (315 to 2064 pmol/L). Mean individual coefficient of variation was 19% (95% CI: 16 to 21%) and group coefficient of variation was 43% (95% CI: 41 to 46%), with index of individuality at 0.44. The breed-specific reference interval was 275 to 2100 pmol/L. In the validation group, 93% of NT-proBNP measurements from healthy dogs were within the reference interval. NT-proBNP measurements exceeded the reference interval in 82% of dogs with dilated cardiomyopathy. The upper bound of the reference interval (2100 pmol/L) had a positive predictive value of 90% and a negative predictive value of 87% for identification of dilated cardiomyopathy in this population.

CLINICAL SIGNIFICANCE

Breed-specific reference intervals might improve the diagnostic accuracy of NT-proBNP measurement. Applying the currently recommended general cut-off value to Labradors is likely to result in frequent false positives and diagnosis would be improved by application of the new breed-specific reference interval calculated here.

UK national cohort of anal cancer treated with intensity-modulated radiotherapy: One-year oncological and patient-reported outcomes

BACKGROUND

Concurrent chemoradiotherapy is the standard treatment for anal cancer. Following national UK implementation of intensity-modulated radiotherapy (IMRT), this prospective, national cohort evaluates the one-year oncological outcomes and patient-reported toxicity outcomes (PRO) after treatment.

MATERIALS AND METHODS

A national cohort of UK cancer centers implementing IMRT was carried out between February to July 2015. Cancer centers provided data on oncological outcomes, including survival, and disease and colostomy status at one-year. EORTC-QLQ core (C30) and colorectal (CR29) questionnaires were completed at baseline and one-year followup. The PRO scores at baseline and one year were compared.

RESULTS

40 UK Cancer Centers returned data with a total of 187 patients included in the analysis. 92% received mitomycin with 5-fluorouracil or capecitabine. One-year overall survival was 94%; 84% were disease-free and 86% colostomy-free at one-year followup. At one year, PRO results found significant improvements in buttock pain, blood and mucus in stools, pain, constipation, appetite loss, and health anxiety compared to baseline. No significant deteriorations were reported in diarrhea, bowel frequency, and flatulence. Urinary symptom scores were low at one year. Moderate impotence symptoms at baseline remained at one year, and a moderate deterioration in dyspareunia reported.

CONCLUSIONS

With national anal cancer IMRT implementation, at this early pre-defined time point, one-year oncological outcomes were reassuring and resulted in good disease-related symptom control. one-year symptomatic complications following CRT for anal cancer using IMRT techniques appear to be relatively mild. These PRO results provide a basis to benchmark future studies.

A multivariate analysis of women's mating strategies and sexual selection on men's facial morphology

The strength and direction of sexual selection via female choice on masculine facial traits in men is a paradox in human mate choice research. While masculinity may communicate benefits to women and offspring directly (i.e. resources) or indirectly (i.e. health), masculine men may be costly as long-term partners owing to lower paternal investment. Mating strategy theory suggests women's preferences for masculine traits are strongest when the costs associated with masculinity are reduced. This study takes a multivariate approach to testing whether women's mate preferences are context-dependent. Women (n = 919) rated attractiveness when considering long-term and short-term relationships for male faces varying in beardedness (clean-shaven and full beards) and facial masculinity (30% and 60% feminized, unmanipulated, 30% and 60% masculinized). Participants then completed scales measuring pathogen, sexual and moral disgust, disgust towards ectoparasites, reproductive ambition, self-perceived mate value and the facial hair in partners and fathers. In contrast to past research, we found no associations between pathogen disgust, self-perceived mate value or reproductive ambition and facial masculinity preferences. However, we found a significant positive association between moral disgust and preferences for masculine faces and bearded faces. Preferences for beards were lower among women with higher ectoparasite disgust, providing evidence for ectoparasite avoidance hypothesis. However, women reporting higher pathogen disgust gave higher attractiveness ratings for bearded faces than women reporting lower pathogen disgust, providing support for parasite-stress theories of sexual selection and mate choice. Preferences for beards were also highest among single and married women with the strongest reproductive ambition. Overall, our results reflect mixed associations between individual differences in mating strategies and women's mate preferences for masculine facial traits.

Effects of Pyruvic Acid, Succinic Acid, and Oregano Essential Oil on Salmonella, Natural Microflora, and Quality of Raw Ground Chicken

ObjectivesThe growing stringency of regulations related to pathogens in raw poultry and increasing consumer demand for more natural food ingredients makes it imperative to explore alternative antimicrobial agents. The aim of this study was to assess the anti-Salmonella effect of combinations of succinate or pyruvic acid with oregano essential oil in raw ground chicken. Additionally, their effect on natural microflora and quality of ground chicken over simulated retail display was evaluated.Materials and MethodsNalidixic acid (NA) adapted Salmonella Typhimurium was inoculated on skin-on broiler breast meat pieces. The antimicrobial treatments given to meat were 2 and 3% pyruvic acid (PA) or monosodium succinate (SA) in combination with 0.5% essential oil (EO). Agar at the concentration of 0.05% was added to water used to prepare antimicrobial solutions to disperse the essential oil. Mode of antimicrobial treatment was 30 s dip. The meat was then ground and evaluated for pathogen reduction. Data were analyzed using 1-way ANOVA. Surviving Salmonella were recovered on XLT-4 with 50 ppm NA. Non-inoculated meat was similarly treated with antimicrobial dip and ground. Ground chicken was packaged in foam trays with PVC overwrap, and evaluated for mesophilic aerobic plate count (APC), psychrotrophic count (PC), pH, instrumental color (CIE L*, a*, and b*), and expressible moisture over 8 d of simulated retail display.A factorial design was assigned to the experiment with antimicrobial treatments and display days as the fixed effect factors. Data were analyzed using a mixed general linear model that considered replicates as a random effect in addition to the mentioned fixed effects. All trials were conducted in three replicates.ResultsMaximum reduction obtained in Salmonella counts from ground chicken was 1.52 log CFU/g and 0.98 log CFU/g, resulting from 3% SA + 0.5% EO, and 3% PA + 0.5% EO, respectively. Three percent SA + 0.5% EO treatment resulted in ground chicken with approximately 1.2 log CFU/g lower APC on Day 8 that was significantly lower (P < 0.05) than all other treatments. This treatment also resulted in less pH variation over the entire shelf life duration and lighter color of ground meat on Day 8.ConclusionThese results indicate that combination of monosodium succinate and oregano essential oil provides effective reduction of Salmonella and improved raw quality of ground chicken. This antimicrobial combination can be employed as a clean label ingredient for raw chicken applications.

Anti-Salmonella Effects of Pyruvic and Succinic Acid in Combination with Oregano Essential Oil

ObjectivesEffective decontamination approaches will aid in improving safety of poultry products and help processors comply with pathogen performance standards. Increasing consumer demand for clean label and more natural ingredients presents a scope to explore alternative decontamination approaches for meat and food contact surfaces. This study aimed to evaluate the antimicrobial efficacy of combinations of pyruvic acid (PA), succinic acid (SA), and oregano essential oil (EO) against Salmonella Typhimurium in suspensions, cells inoculated on raw chicken, and cells attached to steel.Materials and MethodsMinimum bactericidal concentration (MBC) assays were conducted in Mueller-Hinton broth (5 mL). Bacterial cells were added to broth suspensions of antimicrobial agents or their combinations. A contact time not exceeding 10 s was provided. Surviving bacteria were recovered on tryptic soy agar (TSA). Bacterial inactivation was confirmed by enrichment in D/E broth. Experiment involved completely randomized design with each concentration of organic acid and essential oil being considered as one level. Data were analyzed using 1-way ANOVA. Aqueous solutions of PA, SA, EO, and the mixtures of PA+EO and SA+EO were prepared using 0.05% agar to suspend the essential oil. Skin-on raw chicken breast meat pieces (2.5 cu cm) were used as a substrate to inoculate nalidixic acid (NA) adapted Salmonella cells. Pieces were treated with antimicrobial agents for 30 s by dipping, and surviving Salmonella were recovered using D/E broth on XLT-4 agar with 50 ppm NA. Four different experiments with variable acid and essential oil concentrations were performed and data were analyzed using 1-way ANOVA. Each experiment included an inoculated untreated control. Stainless steel coupons (2 × 5 cm) were used as a substrate for Salmonella attachment. Cells were allowed to grow and attach on coupons submerged in tryptic soy broth for 24 h. Coupons were rinsed to remove planktonic cells. Attached cells remaining on the coupon were dip treated with antimicrobial agents for 5 min. Surviving cells were recovered on TSA. For antimicrobial treatments leading to no cell recovery, additional experiments were performed. The recovery broth was enriched in tryptic soy broth and streaked on TSA to confirm inactivation. Three different experiments were conducted while including their respective inoculated and untreated controls and analyzed using 1-way ANOVA. All experiments were conducted in three replicates.ResultsMBC for was found to be PA (0.5%), SA(3%), EO (0.04%), PA+EO (0.25 + 0.02%), SA+EO (0.25 + 0.02%), respectively. 1% PA + 0.08% EO combination produced the maximum reduction (1.42 ± 0.11 log CFU/cm2) followed by 6% SA + 0.08% EO (1.02 ± 0.08 log CFU/cm2) in Salmonella populations on raw chicken. More than 6 log CFU/coupon of attached Salmonella were inactivated by mixtures of 0.25% PA + 0.02% EO and 1.5% SA + 0.02% EO.ConclusionThe combinations of PA+EO and SA+EO both exhibited strong anti-Salmonella activity in cell suspensions, on cells attached to stainless steel, and were effective in reducing Salmonella populations on raw chicken. Therefore, these antimicrobial combinations merit further research for raw poultry, meat, and other sanitation applications.

Atmospheric Spray Freeze Drying of Sugar Solution With Phage D29

Therapeutic bacteriophages offer a potential alternative approach in the treatment of drug resistant bacteria. In the present study, we examine the ability of atmospheric spray freeze-drying (ASFD) to process bacteriophage D29 into a solid dry formulation. Bacteriophage D29 is of particular interest due to its ability to infect Mycobacterium tuberculosis. A sugar solution containing bacteriophage D29 was sprayed and instantly frozen in a cold chamber. Cold drying gas was then passed through the chamber at a high flow rate and atmospheric pressure. Convective transport combined with the low temperature of the drying gas results in sublimation of ice, yielding a free-flowing, porous powder. The bacteriophages were atmospheric spray freeze-dried in solutions with varying concentrations of trehalose and mannitol. A solution of trehalose and mannitol at a mass ratio of 7:3 and a total mass concentration of 100 mg/mL led to powder with 4.9 ± 0.1% moisture content and an acceptable titer reduction of ∼0.6 logs. In comparison, a pure trehalose solution and a 1:1 ratio of trehalose and mannitol both had titer reductions of >1.5 logs. Spectroscopic analysis showed that trehalose in the powder was amorphous while mannitol completely crystallized during the drying process, both of which are desirable for preserving phage viability and storage in powders. The results highlight the potential for using ASFD as an alternative process in preserving biopharmaceutical products.

Continuing Education and New Zealand Anaesthetists: An Analysis of Current Practice and Future Needs

A survey of Continuing Medical Education (CME) of New Zealand anaesthetists was undertaken to identify current patterns of participation, usefulness of different activities, evidence of effectiveness, motivators and barriers to participation and to define future CME needs.

The response rate was 74% and showed high levels of participation in a range of CME activities. Ratings for usefulness differed significantly between these activities. Respondents identified specific changes they had made to their practice as a result of CME, providing strong evidence for its effectiveness.

Anaesthetists valued interactive methods of learning that were relevant to clinical practice. The most commonly reported motivators for participation were accreditation requirements and keeping up to date, while other work commitments were the commonest impediment. In this survey, interactive educational interventions were seen as useful, a finding consistent with systematic reviews of the effectiveness of CME in changing physician behaviour. Such reviews conclude that there is no evidence that conferences are effective in changing physician behaviour, yet respondents to this survey attributed many changes in practice to their attendance at a conference.

Analysis of the needs of NZ anaesthetists supports increasing the number of workshops and interactive sessions and promoting smaller meetings and practice-based activities. The survey provides a basis for designing a future program of CME for New Zealand.

A data citation roadmap for scientific publishers

This article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP), a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of FORCE11.org and the NIH BioCADDIE program. The structure of the roadmap presented here follows the "life of a paper" workflow and includes the categories Pre-submission, Submission, Production, and Publication. The roadmap is intended to be publisher-agnostic so that all publishers can use this as a starting point when implementing JDDCP-compliant data citation. Authors reading this roadmap will also better know what to expect from publishers and how to enable their own data citations to gain maximum impact, as well as complying with what will become increasingly common funder mandates on data transparency.

Publishing peer review materials

Publishing peer review materials alongside research articles promises to make the peer review process more transparent as well as making it easier to recognise these contributions and give credit to peer reviewers. Traditionally, the peer review reports, editors letters and author responses are only shared between the small number of people in those roles prior to publication, but there is a growing interest in making some or all of these materials available. A small number of journals have been publishing peer review materials for some time, others have begun this practice more recently, and significantly more are now considering how they might begin. This article outlines the outcomes from a recent workshop among journals with experience in publishing peer review materials, in which the specific operation of these workflows, and the challenges, were discussed. Here, we provide a draft as to how to represent these materials in the JATS and Crossref data models to facilitate the coordination and discoverability of peer review materials, and seek feedback on these initial recommendations.

BACCHUS: A randomised non-comparative phase II study of neoadjuvant chemotherapy (NACT) in patients with locally advanced rectal cancer (LARC)

BACKGROUND

Chemoradiation (CRT) or short-course radiotherapy (SCRT) are standard treatments for locally advanced rectal cancer (LARC). We evaluated the efficacy/safety of two neoadjuvant chemotherapy (NACT) regimens as an alternative prior to total mesorectal excision (TME).

METHODS/DESIGN

This multi-centre, phase II trial in patients with magnetic resonance imaging (MRI) defined high-risk LARC (>cT3b, cN2+ or extramural venous invasion) randomised patients (1:1) to FOLFOX + Bevacizumab (Arm 1) or FOLFOXIRI + bevacizumab (Arm 2) every 14 days for 6 cycles prior to surgery. Patients were withdrawn if positron emission tomography (PET) standardised uptake value (SUV) after 3 cycles failed to decrease by >30% or increased compared to baseline. Primary endpoint was pathological complete response rate (pCR). Secondary endpoints included adverse events (AE) and toxicity. Neoadjuvant rectal (NAR) scores based on "T" and "N" downstaging were calculated.

FINDINGS

Twenty patients aged 18-75 years were randomised. The trial stopped early because of poor accrual. Seventeen patients completed all 6 cycles of NACT. One stopped due to myocardial infarction, 1 poor response on PET (both received CRT) and 1 committed suicide. 11 patients had G3 AE, 1 G4 AE (neutropenia), and 1 G5 (suicide). pCR (the primary endpoint) was 0/10 for Arm 1 and 2/10 for Arm 2 i.e. 2/20 (10%) overall. Median NAR score was 14·9 with 5 (28%), 7 (39%), and 6 (33%) having low, intermediate, or high scores. Surgical morbidity was acceptable (1/18 wound infection, no anastomotic leak/pelvic sepsis/fistulae). The 24-month progression-free survival rate was 75% (95% CI: 60%-85%).

INTERPRETATION

The primary endpoint (pCR rate) was not met. However, FOLFOXIRI and bevacizumab achieved promising pCR rates, low NAR scores and was well-tolerated. This regimen is suitable for testing as the novel arm against current standards of SCRT and/or CRT in a future trial.

32 and you - genetic testing for dental disorders

Genetic testing for serious illness and disease is becoming increasingly embedded in NHS healthcare. It can confirm a clinical diagnosis or guide therapy. Genetic testing for dental developmental disorders has moved beyond the realms of rarified grant-funded research groups and is now sufficiently rapid and affordable to be offered as part of a clinical service in some dental teaching hospitals. The first presentation of some genetic diseases may be in the dental surgery, so the family dentist should hone their diagnostic skills to identify patients who would benefit from referral to a genetics service. While diagnosis may sometimes guide treatment, there are now examples where it can even lead to cure. This article aims to describe some concepts and issues that a dentist should consider when referring for testing for a genetic dental disorder, and proposes that this subject area should be expanded in the dental undergraduate and postgraduate curricula in the UK.

Management of Barrett's esophagus with low-grade dysplasia

Barrett's esophagus progresses to esophageal adenocarcinoma in a stepwise histological fashion of no dysplasia, low grade dysplasia, high grade dysplasia and cancer. Hence the progression to cancer from various histological stages is different. Progression to cancer from low grade dysplasia is highly variable in the literature due to high inter-observer variability between pathologists in diagnosing it. Studies have shown the utility of having confirmation of low grade dysplasia by expert pathologists or documenting its persistence on two subsequent endoscopies in order to unify the diagnosis. The treatment of low grade dysplasia is variable. In this article we summarize the diagnosis, evaluation and management of low grade dysplasia in Barrett's Esophagus.