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7. The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research

Author

Percie du Sert, Nathalie, Hurst, Viki, Ahluwalia, Amrita, Alam, Sabina, Avey, Marc T., Baker, Monya, Browne, William J., Clark, Alejandra, Cuthill, Innes C., Dirnagl, Ulrich, Emerson, Michael, Garner, Paul, Holgate, Stephen T., Howells, David W., Karp, Natasha A., Lazic, Stanley E., Lidster, Katie, MacCallum, Catriona J., Macleod, Malcolm, Pearl, Esther J., Petersen, Ole H., Rawle, Frances, Reynolds, Penny, Rooney, Kieron, Sena, Emily S., Silberberg, Shai D., Steckler, Thomas, and Würbel, Hanno

Published
2020
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9. UK consensus on pre-clinical vascular cognitive impairment functional outcomes assessment: Questionnaire and workshop proceedings

Author

McFall, Aisling, Hietamies, Tuuli M, Bernard, Ashton, Aimable, Margaux, Allan, Stuart M, Bath, Philip M, Brezzo, Gaia, Carare, Roxana O, Carswell, Hilary V, Clarkson, Andrew N, Currie, Gillian, Farr, Tracy D, Fowler, Jill H, Good, Mark, Hainsworth, Atticus H, Hall, Catherine, Horsburgh, Karen, Kalaria, Rajesh, Kehoe, Patrick, Lawrence, Catherine, Macleod, Malcolm, McColl, Barry W, McNeilly, Alison, Miller, Alyson A, Miners, Scott, Mok, Vincent, O’Sullivan, Michael, Platt, Bettina, Sena, Emily S, Sharp, Matthew, Strangward, Patrick, Szymkowiak, Stefan, Touyz, Rhian M, Trueman, Rebecca C, White, Claire, McCabe, Chris, Work, Lorraine M, and Quinn, Terence J

Published
2020
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20. The IMPROVE Guidelines (Ischaemia Models: Procedural Refinements Of in Vivo Experiments)

Author

Percie du Sert, Nathalie, Alfieri, Alessio, Allan, Stuart M, Carswell, Hilary VO, Deuchar, Graeme A, Farr, Tracy D, Flecknell, Paul, Gallagher, Lindsay, Gibson, Claire L, Haley, Michael J, Macleod, Malcolm R, McColl, Barry W, McCabe, Christopher, Morancho, Anna, Moon, Lawrence DF, O’Neill, Michael J, Pérez de Puig, Isabel, Planas, Anna, Ragan, C Ian, Rosell, Anna, Roy, Lisa A, Ryder, Kathryn O, Simats, Alba, Sena, Emily S, Sutherland, Brad A, Tricklebank, Mark D, Trueman, Rebecca C, Whitfield, Lucy, Wong, Raymond, and Macrae, I Mhairi

Published
2017
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21. Designing, conducting, and reporting reproducible animal experiments.

Author

Wilson, Emma, Ramage, Fiona J., Wever, Kimberley E., Sena, Emily S., Macleod, Malcolm R., and Currie, Gillian L.

Subjects
ANIMAL experimentation, REPRODUCIBLE research, SCIENTIFIC community, PREPRINTS, EXPERIMENTAL design
Abstract

In biomedicine and many other fields, there are growing concerns around the reproducibility of research findings, with many researchers bein g unable to replicate their own or others' results. This raises important questions as to the validity and usefulness of much published research. In this review, we aim to engage researchers in the issue of research reproducibility and equip them with the necessary tools to increase the reproducibility of their research. We first high light the causes and potential impact of non-reproducible research and emphasise the benefits of working reproducibly for the researcher and broader research community. We address specific targets for improvement and steps that individual researchers can take to increase the reproducibility of their work. We next provide recommendations for improving the design and conduct of experiments, focusing on in vivo animal experiments. We describe common sources of poor internal validity of experiments and offer practical guidance for limiting these potential sources of bias at different experi mental stages, as well as discussing other important considerations during experimental design. We provide a list of key resources available to researchers to improve experimental design, conduct, and reporting. We then discuss the importance of open research practices such as study preregistration and the use of preprints and describe recommendations around data management and sharing. Our review emphasises the importance of reproducible work and aims to empower every individual researcher to contribute to the reproducibility of research in their field. [ABSTRACT FROM AUTHOR]

Published
2023
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22. Letter to the editor - round table unites to tackle culture change in an effort to improve animal research reporting

Author

Osborne, Nicola J., Ritskes-Hoitinga, Merel, Ahluwahlia, Amrita, Alam, Sabina, Brown, Matthew, Henderson, Hayley, de Leeuw, Wim, Marsh, Joan, Moher, David, van Oort, Erica, Rawle, Frances, Riederer, Beat M., Sanchez-Morgado, Jose, Sena, Emily S., Struthers, Caroline, Westmore, Matthew, Avey, Marc T., Kalman, Rony, O’Connor, Annette, Sargeant, Jan, Petrie, Anja, and Smith, Adrian

Published
2017
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30. Community consensus on core open science practices to monitor in biomedicine.

Author

Cobey, Kelly D., Haustein, Stefanie, Brehaut, Jamie, Dirnagl, Ulrich, Franzen, Delwen L., Hemkens, Lars G., Presseau, Justin, Riedel, Nico, Strech, Daniel, Alperin, Juan Pablo, Costas, Rodrigo, Sena, Emily S., van Leeuwen, Thed, Ardern, Clare L., Bacellar, Isabel O. L., Camack, Nancy, Britto Correa, Marcos, Buccione, Roberto, Cenci, Maximiliano Sergio, and Fergusson, Dean A.

Subjects
COMMUNITIES, MEDICAL research, PARTICIPANT observation, INTERNET surveys, OPEN scholarship
Abstract

The state of open science needs to be monitored to track changes over time and identify areas to create interventions to drive improvements. In order to monitor open science practices, they first need to be well defined and operationalized. To reach consensus on what open science practices to monitor at biomedical research institutions, we conducted a modified 3-round Delphi study. Participants were research administrators, researchers, specialists in dedicated open science roles, and librarians. In rounds 1 and 2, participants completed an online survey evaluating a set of potential open science practices, and for round 3, we hosted two half-day virtual meetings to discuss and vote on items that had not reached consensus. Ultimately, participants reached consensus on 19 open science practices. This core set of open science practices will form the foundation for institutional dashboards and may also be of value for the development of policy, education, and interventions. The state of open science needs to be monitored to track changes over time and identify areas to create interventions to drive improvements. This Consensus View identifies 19 open science practices that will form the foundation for institutional dashboards for monitoring progress. [ABSTRACT FROM AUTHOR]

Published
2023
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31. Screening for in vitro systematic reviews: a comparison of screening methods and training of a machine learning classifier.

Author

Wilson, Emma, Cruz, Florenz, Maclean, Duncan, Ghanawi, Joly, McCann, Sarah K., Brennan, Paul M., Jing Liao, Sena, Emily S., and Macleod, Malcolm

Subjects
MACHINE learning, TEXT mining, IN vitro studies
Abstract

Objective: Existing strategies to identify relevant studies for systematic review may not perform equally well across research domains. We compare four approaches based on either human or automated screening of either title and abstract or full text, and report the training of a machine learning algorithm to identify in vitro studies from bibliographic records. Methods: We used a systematic review of oxygen-glucose deprivation (OGD) in PC-12 cells to compare approaches. For human screening, two reviewers independently screened studies based on title and abstract or full text, with disagreements reconciled by a third. For automated screening, we applied text mining to either title and abstract or full text. We trained a machine learning algorithm with decisions from 2000 randomly selected PubMed Central records enriched with a dataset of known in vitro studies. Results: Full-text approaches performed best, with human (sensitivity: 0.990, specificity: 1.000 and precision: 0.994) outperforming text mining (sensitivity: 0.972, specificity: 0.980 and precision: 0.764). For title and abstract, text mining (sensitivity: 0.890, specificity: 0.995 and precision: 0.922) outperformed human screening (sensitivity: 0.862, specificity: 0.998 and precision: 0.975). At our target sensitivity of 95% the algorithm performed with specificity of 0.850 and precision of 0.700. Conclusion: In this in vitro systematic review, human screening based on title and abstract erroneously excluded 14% of relevant studies, perhaps because title and abstract provide an incomplete description of methods used. Our algorithm might be used as a first selection phase in in vitro systematic reviews to limit the extent of full text screening required. [ABSTRACT FROM AUTHOR]

Published
2023
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50. Epidemiology and reporting characteristics of preclinical systematic reviews.

Author

Hunniford, Victoria T., Montroy, Joshua, Fergusson, Dean A., Avey, Marc T., Wever, Kimberley E., McCann, Sarah K., Foster, Madison, Fox, Grace, Lafreniere, Mackenzie, Ghaly, Mira, Mannell, Sydney, Godwinska, Karolina, Gentles, Avonae, Selim, Shehab, MacNeil, Jenna, Sikora, Lindsey, Sena, Emily S., Page, Matthew J., Macleod, Malcolm, and Moher, David

Subjects
ANIMAL experimentation, ANIMAL species, EPIDEMIOLOGY, TEST validity
Abstract

In an effort to better utilize published evidence obtained from animal experiments, systematic reviews of preclinical studies are increasingly more common—along with the methods and tools to appraise them (e.g., SYstematic Review Center for Laboratory animal Experimentation [SYRCLE's] risk of bias tool). We performed a cross-sectional study of a sample of recent preclinical systematic reviews (2015–2018) and examined a range of epidemiological characteristics and used a 46-item checklist to assess reporting details. We identified 442 reviews published across 43 countries in 23 different disease domains that used 26 animal species. Reporting of key details to ensure transparency and reproducibility was inconsistent across reviews and within article sections. Items were most completely reported in the title, introduction, and results sections of the reviews, while least reported in the methods and discussion sections. Less than half of reviews reported that a risk of bias assessment for internal and external validity was undertaken, and none reported methods for evaluating construct validity. Our results demonstrate that a considerable number of preclinical systematic reviews investigating diverse topics have been conducted; however, their quality of reporting is inconsistent. Our study provides the justification and evidence to inform the development of guidelines for conducting and reporting preclinical systematic reviews. A cross sectional study of a sample of recent preclinical systematic reviews reveals deficiencies in reporting and provides the justification and evidence to inform the development of specific guidelines for conducting and reporting preclinical systematic reviews. [ABSTRACT FROM AUTHOR]

Published
2021
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