Web Resources for SARS-CoV-2 Genomic Database, Annotation, Analysis and Variant Tracking.

The SARS-CoV-2 genomic data continue to grow, providing valuable information for researchers and public health officials. Genomic analysis of these data sheds light on the transmission and evolution of the virus. To aid in SARS-CoV-2 genomic analysis, many web resources have been developed to store, collate, analyze, and visualize the genomic data. This review summarizes web resources used for the SARS-CoV-2 genomic epidemiology, covering data management and sharing, genomic annotation, analysis, and variant tracking. The challenges and further expectations for these web resources are also discussed. Finally, we highlight the importance and need for continued development and improvement of related web resources to effectively track the spread and understand the evolution of the virus.

An open chat with Cecília Maria Arraiano.

Professor Cecília Maria Arraiano directs a research group named 'Control of Gene Expression' at Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Oeiras, Portugal. She started her scientific journey at the University of Lisbon, where she graduated in Biology, before completing her PhD in Genetics as a Fulbright-Hays Fellow at the University of Georgia, Athens, USA. After a postdoc in the USA, she returned to Lisbon to establish her own lab. She has authored close to 200 publications mainly in the field of RNA degradation mechanisms, with a focus on enzymes and RNA chaperones that mediate RNA decay in microorganisms. She has received several prizes and is an active member of prestigious organizations. Namely, she is an EMBO member, Fellow of the European Academy of Microbiology, Fellow of the American Academy of Microbiology, and member of the Portuguese Academy of Sciences. In addition, Prof Arraiano has chaired the FEBS Working Group on Women in Science from 2014 to 2022. In this fascinating interview, she discusses her research, her experience working in the USA and Portugal, and the importance of initiatives to support women in science.

Adapting Patient and Public Involvement processes in response to the Covid-19 pandemic.

BACKGROUND: The COVID-19 pandemic brought rapid and major changes to research, and those wishing to carry out Patient and Public Involvement (PPI) activities faced challenges, such as restrictions on movement and contact, illness, bereavement and risks to potential participants. Some researchers moved PPI to online settings during this time but remote consultations raise, as well as address, a number of challenges. It is important to learn from PPI undertaken in this period as face-to-face consultation may no longer be the dominant method for PPI. METHODS: UK stay-at-home measures announced in March 2020 necessitated immediate revisions to the intended face-to-face methods of PPI consultation for the ESORT Study, which evaluated emergency surgery for patients with common acute conditions. PPI plans and methods were modified to all components being online. We describe and reflect on: initial plans and adaptation; recruitment; training and preparation; implementation, contextualisation and interpretation. Through first-hand accounts we show how the PPI processes were developed, experienced and viewed by different partners in the process. DISCUSSION AND CONCLUSIONS: While concerns have been expressed about the possible limiting effects of forgoing face-to-face contact with PPI partners, we found important benefits from the altered dynamic of the online PPI environment. There were increased opportunities for participation which might encourage the involvement of a broader demographic, and unexpected benefits in that the online platform seemed to have a 'democratising' effect on the meetings, to the benefit of the PPI processes and outcomes. Other studies may however find that their particular research context raises particular challenges for the use of online methods, especially in relation to representation and inclusion, as new barriers to participation may be raised. It is important that methodological challenges are addressed, and researchers provide detailed examples of novel methods for discussion and empirical study. PATIENT AND PUBLIC CONTRIBUTION: We report a process which involved people with lived experience of emergency conditions and members of the public. A patient member was involved in the design and implementation, and two patients with lived experience contributed to the manuscript.

Tolerating bad health research: the continuing scandal.

BACKGROUND: At the 2015 REWARD/EQUATOR conference on research waste, the late Doug Altman revealed that his only regret about his 1994 BMJ paper 'The scandal of poor medical research' was that he used the word 'poor' rather than 'bad'. But how much research is bad? And what would improve things? MAIN TEXT: We focus on randomised trials and look at scale, participants and cost. We randomly selected up to two quantitative intervention reviews published by all clinical Cochrane Review Groups between May 2020 and April 2021. Data including the risk of bias, number of participants, intervention type and country were extracted for all trials included in selected reviews. High risk of bias trials was classed as bad. The cost of high risk of bias trials was estimated using published estimates of trial cost per participant. We identified 96 reviews authored by 546 reviewers from 49 clinical Cochrane Review Groups that included 1659 trials done in 84 countries. Of the 1640 trials providing risk of bias information, 1013 (62%) were high risk of bias (bad), 494 (30%) unclear and 133 (8%) low risk of bias. Bad trials were spread across all clinical areas and all countries. Well over 220,000 participants (or 56% of all participants) were in bad trials. The low estimate of the cost of bad trials was £726 million; our high estimate was over £8 billion. We have five recommendations: trials should be neither funded (1) nor given ethical approval (2) unless they have a statistician and methodologist; trialists should use a risk of bias tool at design (3); more statisticians and methodologists should be trained and supported (4); there should be more funding into applied methodology research and infrastructure (5). CONCLUSIONS: Most randomised trials are bad and most trial participants will be in one. The research community has tolerated this for decades. This has to stop: we need to put rigour and methodology where it belongs - at the centre of our science.

Body present... in teaching and health care / Corpo presente... na formação e no cuidado em saúde / Cuerpo presente... en el enseñanza y en cuidado de la salud

A pandemia da COVID-19 nos incitou a produzir uma reflexão a respeito dos conteúdos e modos de sugerir e orientar para a atividade física, haja vista ela não prevenir a infecção e, em ambientes fechados, favorecer a contaminação do vírus. De outra perspectiva, os corpos "das ruas" não se satisfazem com as instruções e respostas dos manuais e guias de atividade física. Nesse sentido, os profissionais de saúde precisam abrir os olhos, os corações e as mentes para a construção de movimentos de composição com as cidades e as lutas em defesa de todas as vidas e não se soltar ou se perder dos estudantes, potenciais cuidadores no futuro próximo. O que propomos para este ensaio é fazer pensar sobre o que nos passa enquanto docente e profissionais-pesquisadoras preocupadas e envolvidas com os processos de formação, especialmente no campo da saúde, a partir de ponderações teórico-conceituais sobre nossas experiências (AU).

The COVID-19 pandemic has prompted us to produce thought upon the content and modes of suggesting and directing physical activity, as it does not prevent infection, and, indoors, promotes contamination from the virus. From another perspective, the bodies of the "streets" are not satisfied with the instructions and answers of the manuals and physical activity guides. In this sense, health professionals need to open their eyes, hearts and minds to build compositional movements with the cities and struggles in defense of everybody's lives, holding onto and not getting lost from students, the potential carers in the near future. What we propose for this essay is to make us think about what happens to us as a professor and professionals-researches concerned and involved with the education processes, specially in the field of health, based on theoretical and conceptual considerations about our experiences (AU).

La pandemia COVID-19 nos incitó a reflexionar sobre los contenidos y formas de sugerir y orientar las actividades física, em vista de no prevenir la infección y, en ambientes cerrados, favorecer la contaminación por virus. Desde otra perspectiva, los cuerpos "de las calles" no están satisfechos con las instrucciones y respuestas de los manuales y guías de actividad física. En este sentido, los profesionales de la salud necesitan abrir los ojos, el corazón y la mente para construir movimientos de composición con ciudades y luchas en defensa de todas las vidas y no soltarse o perderse de los estudiantes, potenciales cuidadores en el futuro próximo.Lo que proponemos para este ensayo es hacernos reflexionar sobre lo que nos sucede como profesores-investigadores interesados e involucrados en los procesos de formación, especialmente en el campo de la salud, a partir de consideraciones teórico-conceptuales sobre nuestras experiencias (AU).

Decentralised clinical trials: ethical opportunities and challenges.

Fuelled by adaptations to clinical trial implementation during the COVID-19 pandemic, decentralised clinical trials are burgeoning. Decentralised clinical trials involve many digital tools to facilitate research without physical contact between research teams and participants at various stages, such as recruitment, enrolment, informed consent, administering study interventions, obtaining patient-reported outcome measures, and safety monitoring. These tools can provide ways of ensuring participants' safety and research integrity, while sometimes reducing participant burden and trial cost. Research sponsors and investigators are interested in expanding the use of decentralised clinical trials. The US Food and Drug Administration and other regulators worldwide have issued guidance on how to implement such adaptations. However, there has been little focus on the distinct ethical challenges these trials pose. In this Health Policy report, which is informed by both traditional research ethics and digital ethics frameworks, we group the related ethical issues under three areas requiring increased ethical vigilance: participants' safety and rights, scientific validity, and ethics oversight. Our aim is to describe these issues, offer practical means of addressing them, and prompt the delineation of ethical standards for decentralised trials.

"Tortured phrases" in preprints.

This commentary takes note of the existence of "tortured phrases" (i.e. unspecific jargon or confusing alternative phrases), as indexed in the Tortured Phrases Detector of the Problematic Paper Screener (PPS) (sourced on January 10, 2023) in 213 preprints, 13 of which are related to COVID-19. Select "tortured phrases" in 11 preprints are highlighted, to offer readers an appreciation of this phenomenon. The incorrect representation of jargon in the medical and health literature may risk confusing readers by reducing the impact of effective and precise communication. Whereas some "tortured phrases" might represent simple mistranslations, in other cases, an abundance of such terms in a single preprint might reveal a more serious ethical issue, such as the undeclared use of a paper mill or an unprofessional editing service. This commentary is thus only a spring-board to introduce this linguistic phenomenon and to encourage interested academics to explore more cases, the practical implications of their existence, and even the weaknesses and strengths of PPS. Caution is needed about excessive extrapolation of the existence of "tortured phrases", so as not to automatically associate them with ethical infractions or misconduct.

The endangered physician-scientist and COVID-19.

The COVID-19 pandemic has affected almost every stakeholder in healthcare, including the vulnerable population of clinician investigators known as physician-scientists. In this commentary, Rao et al. highlight the underappreciated challenges and opportunities, and present solutions, for physician-scientists vis-à-vis the uniquely disruptive event of the pandemic.

Galaxy Training: A powerful framework for teaching!

There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.