The quality of methods reporting in parasitology experiments

The importance of selection and reporting of the sex of experimental animals

Biased use of males and females in animal studies or omitting specific details of the sex of animals used in publications limits reproducibility, hampers the pace and likelihood of new discoveries and invites adverse events in ensuing clinical research. Hence unbiased use of males and females in animal studies and specific reporting of animal details are increasingly required by funding bodies and scientific journals worldwide. An analysis to determine how males and females are used in animal studies involving the Commonwealth Scientific and Industrial Research Organisation (CSIRO) was undertaken as part of a process to review and further support best practice. In the study 178 publications that contain animal studies and include CSIRO researchers published between January 2014 and December 2016 were analysed for the sex of animals used. The overall sex distribution was males only 26.4% (47/178), females only 15.7% (28/178), males and females 18.0% (32/178) and sex of animals unspecified 39.9% (71/178). Reasons for this distribution include species biology, farming practices and commercial relevance. Although including sex as an experimental variable provides the most information, using both sexes in an animal study requires careful consideration and planning. Furthermore, there are valid biological and experimental reasons why sex distribution in a study may not be balanced. Biological reasons include cases where the severity of disease in a given model differs between males and females, superior husbandry or production traits in one sex and hermaphroditic species that change sex with age. Examples where experiments can only be undertaken in one sex of animal include animal models of female breast cancer, female reproductive traits, male fertility studies and post-castration welfare outcomes. Where there is no biological or experimental reason for using a single sex of animal, future studies should obtain an estimate of sex effect either from the literature or with a pilot study, and experiments should be planned and reported accordingly.

A guideline for reporting experimental protocols in life sciences

Experimental protocols are key when planning, performing and publishing research in many disciplines, especially in relation to the reporting of materials and methods. However, they vary in their content, structure and associated data elements. This article presents a guideline for describing key content for reporting experimental protocols in the domain of life sciences, together with the methodology followed in order to develop such guideline. As part of our work, we propose a checklist that contains 17 data elements that we consider fundamental to facilitate the execution of the protocol. These data elements are formally described in the SMART Protocols ontology. By providing guidance for the key content to be reported, we aim (1) to make it easier for authors to report experimental protocols with necessary and sufficient information that allow others to reproduce an experiment, (2) to promote consistency across laboratories by delivering an adaptable set of data elements, and (3) to make it easier for reviewers and editors to measure the quality of submitted manuscripts against an established criteria. Our checklist focuses on the content, what should be included. Rather than advocating a specific format for protocols in life sciences, the checklist includes a full description of the key data elements that facilitate the execution of the protocol.

The Road to Reproducibility in Animal Research

Reproducibility of research findings is the hallmark of scientific advance. However, the recently noted lack of reproducibility and transparency of published research using animal models of human biology and disease has alarmed funders, scientists, and the public. Improved reporting of methodology and better use of statistical tools are needed to enhance the quality and utility of published research. Reporting guidelines like Animal Research: Reporting In Vivo Experiments (ARRIVE) have been devised to achieve these goals, but most biomedical research journals, including the JBMR, have not been able to obtain high compliance. Cooperative efforts among authors, reviewers and editors-empowered by increased awareness of their responsibilities, and enabled by user-friendly guidelines-are needed to solve this problem. © 2016 American Society for Bone and Mineral Research.

Bias in the reporting of sex and age in biomedical research on mouse models

In animal-based biomedical research, both the sex and the age of the animals studied affect disease phenotypes by modifying their susceptibility, presentation and response to treatment. The accurate reporting of experimental methods and materials, including the sex and age of animals, is essential so that other researchers can build on the results of such studies. Here we use text mining to study 15,311 research papers in which mice were the focus of the study. We find that the percentage of papers reporting the sex and age of mice has increased over the past two decades: however, only about 50% of the papers published in 2014 reported these two variables. We also compared the quality of reporting in six preclinical research areas and found evidence for different levels of sex-bias in these areas: the strongest male-bias was observed in cardiovascular disease models and the strongest female-bias was found in infectious disease models. These results demonstrate the ability of text mining to contribute to the ongoing debate about the reproducibility of research, and confirm the need to continue efforts to improve the reporting of experimental methods and materials.

DOI:http://dx.doi.org/10.7554/eLife.13615.001

Quality of Reporting and Adherence to ARRIVE Guidelines in Animal Studies for Chagas Disease Preclinical Drug Research: A Systematic Review

Publication of accurate and detailed descriptions of methods in research articles involving animals is essential for health scientists to accurately interpret published data, evaluate results and replicate findings. Inadequate reporting of key aspects of experimental design may reduce the impact of studies and could act as a barrier to translation of research findings. Reporting of animal use must be as comprehensive as possible in order to take advantage of every study and every animal used. Animal models are essential to understanding and assessing new chemotherapy candidates for Chagas disease pathology, a widespread parasitic disease with few treatment options currently available. A systematic review was carried out to compare ARRIVE guidelines recommendations with information provided in publications of preclinical studies for new anti-Trypanosoma cruzi compounds. A total of 83 publications were reviewed. Before ARRIVE guidelines, 69% of publications failed to report any macroenvironment information, compared to 57% after ARRIVE publication. Similar proportions were observed when evaluating reporting of microenvironmental information (56% vs. 61%). Also, before ARRIVE guidelines publication, only 13% of papers described animal gender, only 18% specified microbiological status and 13% reported randomized treatment assignment, among other essential information missing or incomplete. Unfortunately, publication of ARRIVE guidelines did not seem to enhance reporting quality, compared to papers appeared before ARRIVE publication. Our results suggest that there is a strong need for the scientific community to improve animal use description, animal models employed, transparent reporting and experiment design to facilitate its transfer and application to the affected human population. Full compliance with ARRIVE guidelines, or similar animal research reporting guidelines, would be an excellent start in this direction.

Quality of methods reporting in animal models of colitis

BACKGROUND

Current understanding of the onset of inflammatory bowel diseases relies heavily on data derived from animal models of colitis. However, the omission of information concerning the method used makes the interpretation of studies difficult or impossible. We assessed the current quality of methods reporting in 4 animal models of colitis that are used to inform clinical research into inflammatory bowel disease: dextran sulfate sodium, interleukin-10, CD45RB T cell transfer, and 2,4,6-trinitrobenzene sulfonic acid (TNBS).

METHODS

We performed a systematic review based on PRISMA guidelines, using a PubMed search (2000-2014) to obtain publications that used a microarray to describe gene expression in colitic tissue. Methods reporting quality was scored against a checklist of essential and desirable criteria.

RESULTS

Fifty-eight articles were identified and included in this review (29 dextran sulfate sodium, 15 interleukin-10, 5 T cell transfer, and 16 TNBS; some articles use more than 1 colitis model). A mean of 81.7% (SD = ±7.038) of criteria were reported across all models. Only 1 of the 58 articles reported all essential criteria on our checklist. Animal age, gender, housing conditions, and mortality/morbidity were all poorly reported.

CONCLUSIONS

Failure to include all essential criteria is a cause for concern; this failure can have large impact on the quality and replicability of published colitis experiments. We recommend adoption of our checklist as a requirement for publication to improve the quality, comparability, and standardization of colitis studies and will make interpretation and translation of data to human disease more reliable.

Impact of the H275Y and I223V Mutations in the Neuraminidase of the 2009 Pandemic Influenza Virus In Vitro and Evaluating Experimental Reproducibility

The 2009 pandemic H1N1 (H1N1pdm09) influenza virus is naturally susceptible to neuraminidase (NA) inhibitors, but mutations in the NA protein can cause oseltamivir resistance. The H275Y and I223V amino acid substitutions in the NA of the H1N1pdm09 influenza strain have been separately observed in patients exhibiting oseltamivir-resistance. Here, we apply mathematical modelling techniques to compare the fitness of the wild-type H1N1pdm09 strain relative to each of these two mutants. We find that both the H275Y and I223V mutations in the H1N1pdm09 background significantly lengthen the duration of the eclipse phase (by 2.5 h and 3.6 h, respectively), consistent with these NA mutations delaying the release of viral progeny from newly infected cells. Cells infected by H1N1pdm09 virus carrying the I223V mutation display a disadvantageous, shorter infectious lifespan (17 h shorter) than those infected with the wild-type or MUT-H275Y strains. In terms of compensating traits, the H275Y mutation in the H1N1pdm09 background results in increased virus infectiousness, as we reported previously, whereas the I223V exhibits none, leaving it overall less fit than both its wild-type counterpart and the MUT-H275Y strain. Using computer simulated competition experiments, we determine that in the presence of oseltamivir at doses even below standard therapy, both the MUT-H275Y and MUT-I223V dominate their wild-type counterpart in all aspects, and the MUT-H275Y outcompetes the MUT-I223V. The H275Y mutation should therefore be more commonly observed than the I223V mutation in circulating H1N1pdm09 strains, assuming both mutations have a similar impact or no significant impact on between-host transmission. We also show that mathematical modelling offers a relatively inexpensive and reliable means to quantify inter-experimental variability and assess the reproducibility of results.

The explicit mentioning of reporting guidelines in urogynecology journals in 2013: A bibliometric study

AIMS

Poor reporting of research may limit critical appraisal and reproducibility, whereas adherence to reporting guidelines (RG) can guarantee completeness and transparency. We aimed to determine the explicit citing of RGs (CONSORT, PRISMA, STROBE) in urogynecology articles in 2013, the requirements of relevant journals and a potential difference between urogynecology and general gynecology journals.

METHODS

All urogynecologic articles published between January and December 2013 in the journals NAU, IUJ, FPMRS, GREEN, AJOG, and BJOG were included. Issues were searched for systematic reviews, RCTs, cohort studies, case-control studies and cross-sectional studies. Each electronic article was searched for the term PRISMA, CONSORT, or STROBE according to the study design. Instructions to Authors of the six journals were screened for requirement of using RGs.

RESULTS

We included 296 articles (243 observational studies, 40 RCTs, and 13 systematic reviews). The use of PRISMA guidelines was explicitly declared in 54% of systematic reviews, CONSORT guidelines were referenced in 25% of RCTs and STROBE in 1.2% of observational studies. The use of CONSORT is required by all journals except FPMRS. PRISMA and STROBE are only compulsory in the journals GREEN, AJOG, and BJOG. The overall rate of explicit mentioning of RGs comparing urogynecology and general gynecology journals was 6.7% versus 7.1%, respectively.

CONCLUSIONS

The explicit mentioning of RGs was on a relatively low level. A slightly higher adherence was recognized among general gynecology journals compared to urogynecology journals. Stronger efforts should be taken to further promote the use of RGs in urogynecology.