Better reporting for better research: a checklist for reproducibility

A Systematic Approach to Review of in vitro Methods in Brain Tumour Research (SAToRI-BTR): Development of a Preliminary Checklist for Evaluating Quality and Human Relevance

Background

A wide range of human in vitro methods have been developed and there is considerable interest in the potential of these studies to address questions related to clinical (human) use of drugs, and the pathobiology of tumours. This requires agreement on how to assess the strength of evidence available (i.e., quality and quantity) and the human-relevance of such studies. The SAToRI-BTR (Systematic Approach To Review of in vitro methods in Brain Tumour Research) project seeks to identify relevant appraisal criteria to aid planning and/or evaluation of brain tumour studies using in vitro methods.

Objectives

To identify criteria for evaluation of quality and human relevance of in vitro brain tumour studies; to assess the general acceptability of such criteria to senior scientists working within the field.

Methods

Stage one involved identification of potential criteria for evaluation of in vitro studies through: (1) an international survey of brain tumour researchers; (2) interviews with scientists, clinicians, regulators, and journal editors; (3) analysis of relevant reports, documents, and published studies. Through content analysis of findings, an initial list of criteria for quality appraisal of in vitro studies of brain tumours was developed. Stage two involved review of the criteria by an expert panel (Delphi process).

Results

Results of stage one indicated that methods for and quality of review of in vitro studies are highly variable, and that improved reporting standards are needed. 129 preliminary criteria were identified; duplicate and highly context-specific items were removed, resulting in 48 criteria for review by the expert (Delphi) panel. 37 criteria reached agreement, resulting in a provisional checklist for appraisal of in vitro studies in brain tumour research.

Conclusion

Through a systematic process of collating assessment criteria and subjecting these to expert review, SAToRI-BTR has resulted in preliminary guidance for appraisal of in vitro brain tumour studies. Further development of this guidance, including investigating strategies for adaptation and dissemination across different sub-fields of brain tumour research, as well as the wider in vitro field, is planned.

Interpreting and integrating big data in the life sciences

Recent advances in omics technologies have led to the broad applicability of computational techniques across various domains of life science and medical research. These technologies provide an unprecedented opportunity to collect the omics data from hundreds of thousands of individuals and to study the gene–disease association without the aid of prior assumptions about the trait biology. Despite the many advantages of modern omics technologies, interpretations of big data produced by such technologies require advanced computational algorithms. I outline key challenges that biomedical researches are facing when interpreting and integrating big omics data. I discuss the reproducibility aspect of big data analysis in the life sciences and review current practices in reproducible research. Finally, I explain the skills that biomedical researchers need to acquire to independently analyze big omics data.

Balancing Interests of Science, Scientists, and the Publishing Business

In the closely coupled system of diverse interests of science, those of scientists (authors, reviewers, and readers), their organizations (universities, research institutions) and those of publishers, every component is undergoing major changes in the digital era. In reality, these interests are deeply interconnected and long-term dominance of any one of them could hinder progress in many different ways. For science, originality and novelty do not have merit without reproducibility; for scientists, quantity is not a substitute for quality, and if businesses focus only on profit, it will suppress the value of their publications. Science, scientists, and organizations not only coexist, but _cannot exist_ without each other, therefore all participants must adjust their actions to avoid devaluation of the whole. Many efforts are underway to regain this balance, and one possible approach – ours at Precision Nanomedicine – is described here.

State of the Science of Sensory Integration Research With Children and Youth

Many children and youth with and without disabilities are affected by challenges in processing and integrating sensations. Occupational therapy practitioners serve a pivotal role in the evaluation and treatment of this population. This special section of the American Journal of Occupational Therapy includes articles that elucidate the relationship between sensory processing and participation in valued occupations as well as articles that guide best practice, including systematic reviews on common occupational therapy interventions for children and youth with challenges in processing and integrating sensation. This editorial elaborates on key issues for future research.

Toward standard practices for sharing computer code and programs in neuroscience

Computational techniques are central in many areas of neuroscience, and are relatively easy to share. This paper describes why computer programs underlying scientific publications should be shared, and lists simple steps for sharing. Together with ongoing efforts in data sharing, this should aid reproducibility of research.

Why articles are retracted: a retrospective cross-sectional study of retraction notices at BioMed Central

OBJECTIVES

To assess why articles are retracted from BioMed Central journals, whether retraction notices adhered to the Committee on Publication Ethics (COPE) guidelines, and are becoming more frequent as a proportion of published articles.

DESIGN/SETTING

Retrospective cross-sectional analysis of 134 retractions from January 2000 to December 2015.

RESULTS

134 retraction notices were published during this timeframe. Although they account for 0.07% of all articles published (190 514 excluding supplements, corrections, retractions and commissioned content), the rate of retraction is rising. COPE guidelines on retraction were adhered to in that an explicit reason for each retraction was given. However, some notices did not document who retracted the article (eight articles, 6%) and others were unclear whether the underlying cause was honest error or misconduct (15 articles, 11%). The largest proportion of notices was issued by the authors (47 articles, 35%). The majority of retractions were due to some form of misconduct (102 articles, 76%), that is, compromised peer review (44 articles, 33%), plagiarism (22 articles, 16%) and data falsification/fabrication (10 articles, 7%). Honest error accounted for 17 retractions (13%) of which 10 articles (7%) were published in error. The median number of days from publication to retraction was 337.5 days.

CONCLUSIONS

The most common reason to retract was compromised peer review. However, the majority of these cases date to March 2015 and appear to be the result of a systematic attempt to manipulate peer review across several publishers. Retractions due to plagiarism account for the second largest category and may be reduced by screening manuscripts before publication although this is not guaranteed. Retractions due to problems with the data may be reduced by appropriate data sharing and deposition before publication. Adopting a checklist (linked to COPE guidelines) and templates for various classes of retraction notices would increase transparency of retraction notices in future.