What are the best practices? (Has Best Practice)
From The Embassy of Good Science
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[https://www.allea.org/wp-content/uploads/2017/05/ALLEA-European-Code-of-Conduct-for-Research-Integrity-2017.pdf The European Code of Conduct for Research Integrity] defines good practices for training, supervision and mentoring:
"Senior researchers, research leaders and supervisors mentor their team members and offer specific guidance and training to properly develop, design and structure their research activity and to foster a culture of research integrity" +
- Tips to ensure public engagement
- Promoting gender equality in research
- Policy recommendations
- Open access
- Science education at schools +
- The pros and cons of self-regulation and statutory regulation
- Who oversees self-regulation? +
One of the most successful projects is FinnGen — the Finnish genomic revolution. The project serves as an excellent example of how genomics can be integrated into the national health system. It was launched in 2017 through a collaboration among public-private partners, such as universities, hospitals, and national biobanks, and pharmaceutical companies such as AstraZeneca, Bayer, Genentech, Pfizer, and others. The goal of the project is to merge genomic sample data (citizens' data) with health registries. It was launched in 2017 and includes 520,000 individual patient records, representing about 10% of the population. The first and second phases of the project is centered on data collection and analysis. In contrast, the third phase, which started in 2023, is focused on pre- and post-diagnosis, patient responses to therapy, and monitoring biological mechanisms related to genetic markers. (4) +
In areas such as physics, mathematics and economy, preprint servers have been in use for almost 30 years.'"`UNIQ--ref-00000012-QINU`"' In 1991 a centralized automated repository, the arXiv preprint server, was the pioneer in this method of dissemination of research results. It played an important role in physics, astronomy and mathematics, and later was implemented into other research areas.'"`UNIQ--ref-00000013-QINU`"' Significant number of journals has adopted this practice of posting their manuscripts on preprint servers. About 46% of the 2,566 publishers indexed in SHERPA RoMEO support preprint servers.'"`UNIQ--ref-00000014-QINU`"' The Lancet, for example, posts articles to preprint severs from Social Science Research Network (SSRN).'"`UNIQ--ref-00000015-QINU`"'
Preprint servers can be journal (Netprints), non-journal (arXiv), mixed (ResearchGate), subject repositories (Social Sciences Research Network) as well as national and regional servers (Chinese Preprint Server Online).'"`UNIQ--ref-00000016-QINU`"' They can be supported by con-commercial and non-editorial organizations as well. For example, the Welcome Trust in UK has its own preprint server.'"`UNIQ--ref-00000017-QINU`"' Research institutions and funding organizations also can have preprint servers. One of the examples is UK’s Medical Research Council (MRC) that includes the manuscripts posted on preprint servers in biomedical research grant applications.'"`UNIQ--ref-00000018-QINU`"'
Some of the most popular preprint servers are:
-[https://www.biorxiv.org/ BioRxiv] (a preprint repository for the biological sciences);-[https://arxiv.org/ arXiv] (an open access archive operated by Cornell University, containing 1,774,607 articles in the fields of physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering and systems science and economics);-[https://thewinnower.com/ the Winnower] (an open access online publishing platform that offers an open post-publication peer review);-[https://psyarxiv.com/ PsyArXiv] (a preprint server for the field of psychology, launched in 2016 by Cornell University);-[http://www.prepubmed.org/ PrePubMed] (a platform that indexes preprints from PeerJ Preprints, Figshare, bioRxiv, and F1000Research)'"`UNIQ--ref-00000019-QINU`"';-[https://www.medrxiv.org/ medRxiv] (the first preprint server for medicine, launched in 2019 by Yale and BMJ).'"`UNIQ--ref-0000001A-QINU`"'
Longer list of preprint repositories can be found [https://docs.google.com/spreadsheets/d/1zYOy6bcydDZ9G56FKmDzg_pexTarVsJR5hH0KiQGt_I/edit#gid=1494155948 here] and [https://asapbio.org/preprint-servers here].
Although there are some preprint servers for medicine, shortcomings of this practice have to be considered. Medical research findings are often discussed by the media and public, so the media release of an unreviewed work can be harmful.'"`UNIQ--ref-0000001B-QINU`"''"`UNIQ--ref-0000001C-QINU`"' Preprints in medicine also raise ethical questions regarding research with humans, therefore the confidentiality of participants should be protected.'"`UNIQ--ref-0000001D-QINU`"'
Nevertheless, in this time of COVID-19 pandemic preprint servers showed to be a useful tool because of the accelerated dissemination of research results. This is important especially regarding treatments and vaccines.'"`UNIQ--ref-0000001E-QINU`"' From the early stages of the pandemic to the mid October, more than 19,000 preprints were produced.'"`UNIQ--ref-0000001F-QINU`"' We also have to consider that peer reviewed articles published in journals can present low-quality work. One of the examples is article about a Russian vaccine, published in the Lancet,'"`UNIQ--ref-00000020-QINU`"' which instigated objections and an open letter to the authors and the Lancet editor. The objections addressed data presented in the article and called for full availability of the original data in order to evaluate the study and enable reproduction of the research findings.'"`UNIQ--ref-00000021-QINU`"''"`UNIQ--ref-00000022-QINU`"'
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- Ensuring academic independence
- Enabling integrity in research
- Misconduct handling +
According to the Belmont[https://www.hhs.gov/ohrp/regulations-and-policy/belmont-report/read-the-belmont-report/index.html]'"`UNIQ--ref-00000003-QINU`"' report:
· Respect
· Beneficence
· Justice
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*Nowadays, ‘good publication’ is considered to be peer reviewed publication. Since 1830 peer review became systematic and operational and is considered essential for academic publishing in present times.
*Journal editors are responsible for the publication process. Their standards are defined in guidelines of the Committee on Publication Ethics (COPE) which were founded in 1997.
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When qualitative research is intended to generate hypotheses for future research or to test the feasibility and acceptability of interventions, then applying the results is relatively straightforward.
Can the results of qualitative research be applied directly to daily clinical practice? If the study population seems similar enough to one’s own, then the clinician can justifiably consider the usage of the study results to reflect on his or her practice (2). +
Pre-registration of study protocols enhances the transparency of the research process and lends credibility to results. +
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Recommendations of the Finnish National Board on Research Integrity TENK for Research Integrity Advisers and related background organisations1 +
Advisors' range of activities include:
- Supporting the responsible conduct of research
- Providing guidance on the handling of misconduct
- Conducting preliminary ethical reviews +
Some of the most common examples of replication failures come from drug discovery and development. Usually drugs are developed in several stages, beginning with cells and animal studies and ultimately advancing to human trials. Failures in both conceptual and direct replication are frequent in this branch of science. Conceptual failure, for example, can occur when testing a drug that has promising action in animals for the first time in humans'"`UNIQ--ref-00000007-QINU`"''"`UNIQ--ref-00000008-QINU`"', whereas a direct replication failure might occur when testing the same drug on a similar group of people'"`UNIQ--ref-00000009-QINU`"'. Since successful replications enhance public trust in science and medicine, the increasing number of non-replicable studies in various disciplines, mainly psychology, have resulted in what has been described as a “replication crisis” and raised serious concerns'"`UNIQ--ref-0000000A-QINU`"'. A study conducted by a team of 270 scientists at the University of Virginia in Charlottesville showed that only 35 of 100 studies published in one of the prominent psychology journals in 2008 could be replicated'"`UNIQ--ref-0000000B-QINU`"'. Some argue however that there is no such thing as a “replication crisis”;moreover, sometimes the “non-replicability” could be helpful to science'"`UNIQ--ref-0000000C-QINU`"'.
If replication fails, it does not necessarily mean that the original result of the experiment which is being replicated is false. It indicates some unknown factors are different in the replication experiment vs. the original experiment and an attempt should be made to investigate these '"`UNIQ--ref-0000000D-QINU`"''"`UNIQ--ref-0000000E-QINU`"'. If such factors are found (either of a technical or knowledge domain specific nature) they can substantially improve the understanding of the phenomena being studied.
In the last few years, leading scientific institutions in the United States have taken some steps to improve replicability. In 2014, the National Institutes of Health (NIH) provided training modules for postdoctoral fellows and a list of publications regarding replicability on their website, and emphasized addressing transparency in grant applications'"`UNIQ--ref-0000000F-QINU`"'. The National Science Foundation (NSF) and the Institute for Education Sciences (IES) have published Companion Guidelines on Replication and Reproducibility in Education Research in 2018. The guidelines suggest several actions to enhance replicability. For example, proposals for replication studies should guarantee objectivity, pre-registration of the research design and methods should ensure transparency, research should be described in detail, and all research data should be publically available'"`UNIQ--ref-00000010-QINU`"'. Taking these important steps calls for a significant culture shift so that accuracy in research would be valued more than swiftness'"`UNIQ--ref-00000011-QINU`"'.
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There have been some cases of successful study replication. One of the most known cases is deciphering the Rosetta Stone. The Stone which was discovered during the Napoleonic Egyptian Campaign in 1799 contains texts both in Ancient Egyptian (hieroglyphic and Demotic script) and in Ancient Greek. By comparing the Demotic, hieroglyphic and ancient Greek texts, British scholar Thomas Young and French scholar Jean-François Champollion managed to decipher Egyptian hieroglyphic.'"`UNIQ--ref-00000005-QINU`"' Numerous scholars have studied the stone later and the main results have been replicated multiple times.'"`UNIQ--ref-00000006-QINU`"' '"`UNIQ--ref-00000007-QINU`"'
Although there is no consensus in the research community, some research organisations, academic journals and platforms have been encouraging replication in the humanities. One of them is the [https://www.nwo.nl/en/about-nwo Netherlands Organisation for Scientific Research] (NWO). The NWO recognizes that while not all humanities research is suitable for replication, this practice is possible in the empirical humanities and this is what it aims to “encourage and facilitate”.'"`UNIQ--ref-00000008-QINU`"'
Cambridge University based journal [https://www.cambridge.org/core/journals/language-teaching Language Teaching] is also fostering original research articles which replicate previous experimental studies in the field of language learning and teaching.'"`UNIQ--ref-00000009-QINU`"' It emphasizes that replication studies can improve the way we interpret empirical research because they provide a second opinion regarding the hypotheses, methods and results of the original paper.'"`UNIQ--ref-0000000A-QINU`"'
Publishing platform [https://opencontext.org/ Open context], founded by archaeologists, also supports and encourages replication in the humanities.'"`UNIQ--ref-0000000B-QINU`"'
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The aim of all eight scenarios is to allow researchers, research ethics committees ('RECs'), research integrity offices ('RIOs') and research administrators to focus their reflection on core principles and research contexts that enshrine good research practice as well as their local rules and practices. +
Good scientific practices (general)
- Good practices in grant applications
- Ethics in research involving animals +
Clear study design, transparent reporting, proper statistical analysis, ethical approval, and secure data handling. +
The aim of all eight scenarios is to allow researchers, research ethics committees ('RECs'), research integrity offices ('RIOs') and research administrators to focus their reflection on core principles and research contexts that enshrine good research practice as well as their local rules and practices. +
The Concordat to Support Research Integrity lists eight aspects which are important for a good research environment to promote best practices and research integrity.'"`UNIQ--ref-00000002-QINU`"' They state a good research culture should include, as a minimum, the following: <br>
*Have clear policies, practices and procedures to support researchers
*Have research ethics and integrity training, including mentoring opportunities
*Have robust management systems ensuring implementation of policies related to research, its integrity and researchers behaviour
*Create awareness among the standards of behaviour of researchers
*Ensure a system is in place that can identify concerns at an early stage
*Provide support mechanisms for those that need assistance
*Have policies in place ensuring no stigma is attached to those that find they need assistance from their emplyees
*Communicate and implement processes to raise concerns about research integrity
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On an individual level, the most important research metrics are the H-index and the i-10 index. The H-index, also known as Hirsch index, is an author level metric that shows how many articles have been cited a certain number of times. For example, a h-index of 10 shows that the author has 10 articles, each cited at least 10 times.'"`UNIQ--ref-00000003-QINU`"' The i-10 index shows the number of articles an author has published with at least 10 citations.
On a journal level, the impact factor shows an average number of citations per article in two consecutive years.'"`UNIQ--ref-00000004-QINU`"' Other famous journal metric systems are Eigenfactor and the SCImago Journal Rankings.
It is important to note that every metric system has its flaws. As a result, they should not be the only criterion when determining the quality and performance of a particular researcher, article, journal or research project.
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