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ORC'''ID''': [[File:ORCID.png|20px|link=https://orcid.org/0000-0003-3647-5895]] Gnaiger E
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== Acknowledgements ==
:::: I thank [[Tindle-Solomon Lisa |Lisa Tindle-Solomon]], [[Cocco Paolo |Paolo Cocco]], and [[Cardoso Luiza |Luiza Cardoso]] for their invaluable contributions in launching Bioenergetics Communications. Initial steps supported by Horizon 2020 project NextGen-O2k.
== References and weblinks ==
|?Was published in year=Year
::* Bioblast: the mt-information synthase, from Richard Altmann's Bioblasts to mitochondrial physiology - http://www.bioblast.at/index.php/Bioblast:About
::* BEC, Bioenergetics Communications - https://www.bioenergetics-communications.org/
::* COPE, Committee on Publication Ethics - https://publicationethics.org/
::* DORA, Declaration on Research Assessment - https://sfdora.org/
::* Gentle Science - http://www.bioblast.at/index.php/Gentle_Science
::* MiPs, Mitochondrial Physiology Society - http://www.mitophysiology.org
::* MitoFit Preprints: the Open Access preprint server for mitochondrial physiology and bioenergetics - http://www.mitofit.org/index.php/MitoFit_Preprints
::* MitoPedia: high-resolution terminology ― matching measurements at high-resolution - http://www.bioblast.at/index.php/MitoPedia
::* MitoPedia: BEC - https://www.bioblast.at/index.php/MitoPedia:_BEC
::* OA, Open Access directory of Open Access Journals DOAJ - https://doaj.org/
::* OS, Open Science, UNESCO (2021) Draft recommendation on Open Science - https://unesdoc.unesco.org/ark:/48223/pf0000378841
::* Plan S initiative for Open Access publishing - https://www.coalition-s.org/
::* SCI, Science Citation Index - https://mjl.clarivate.com/
== Living Communication ==
Last update 2022-02-04
=== Publication and registration into oblivion ===
::::* ‘''For most published papers, “publication” often just signifies “final registration into oblivion”. .. Only 73 of the many thousands of articles ever published by the 187 BMC-affiliated journals had over 10 000 accesses through their journal Web sites in the last year''’ ([[Young 2008 PLoS Med]]).
::::::* Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. Bioenerg Commun 2020.2:112 pp. https://doi.org/10.26124/bec:2020-0002 - has been accessed '''92 758 times ([[Gnaiger_2020_BEC_MitoPathways |accessed 2022-01-01]])'''
::::::* Gnaiger E et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1. https://doi.org/10.26124/bec:2020-0001.v1 - has been accessed '''35 423 times ([[BEC_2020.1_doi10.26124bec2020-0001.v1 |accessed 2022-01-01]])'''
::::* ''The number of publishing scientists has grown over the years, with over 15 million scientists publishing ≥1 article that was indexed in Scopus in the period 1996–2011. Biomedical research is the most prolific scientific field in this regard. It is practically impossible for even the most knowledgeable expert to maintain direct knowledge of the work done by so many other scientists, even when it comes to his/her core discipline of interest'' ([[Begley 2015 Circ Res]]).
=== Pergamon Press and Elsevier ===
::::* The empire of Pergamon Press was built by Robert Maxwell (in cooperation with Paul Rosbaud) and made him a millionaire. "''In 1991, to finance his impending purchase of the New York Daily News, Maxwell sold Pergamon to its quiet Dutch competitor Elsevier for £440m (£919m today)''" ([[Buranyi 2017 Guardian]]). Several financial scandals emerged since he drowned in 1991. Robert Maxwell is hardly remembered by a later generation of scientists, except in relation to his daughter Ghislaine Maxwell who was convicted on 2021-12-29 linked to several federal crimes including her involvement in a sex-trafficking ring with Jeffrey Epstein, to who's former friends belonged British Prince Andrew, former Prime Minister Tony Blair, or ex-US-presidents Bill Clinton and Donald Trump.
=== Paywalls and journal policies ===
::::* ''The academic publishing industry has a large financial turnover. Its worldwide sales amount to more than USD 19 billion, which positions it between the music industry and the film industry ([[Buranyi 2017 Guardian |4]]). The market is largely dominated by five large publishing houses: Elsevier, Black & Wiley, Taylor & Francis, Springer Nature and SAGE, which control more than 50 % of the market between them. .. The government funds all stages of research production, but must then pay again to have access to the research results'' ([[Hagve 2020 Tidsskr Nor Legeforen]]).
::::* ''A review estimated that only 28 % of all scholarly publications are currently open access , meaning that the vast majority of academic knowledge remains inaccessible without a paid individual or institutional subscription. -- Paywalls thus continue to represent a substantial barrier to freely access medical knowledge'' ([[Day 2020 Res Involv Engagem]]).
::::* ''In current open access publishing models, many of the costs associated with production are passed on to individual researchers who agree to pay a fee should their submission be accepted by the journal. This model has been criticized for the potential to create a twotiered system in which peer review is not the sole deciding factor in whose research gets published, but additionally who can afford the fee '' ([[Day 2020 Res Involv Engagem]]).
::::::* '''''Comment: Ref. 38 (in Day 2020) is a BMJ article with € 33 to access this article for 1 day (excl. VAT)''''' (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048123/ accessed 2021-12-31)
::::* ''Manuscripts are assessed with a fundamentally negative bias: how they may best be rejected to promote the presumed selectivity of the journal'' ([[Young 2008 PLoS Med]]).
=== Is open access a misnomer? ===
::::* Floyd L, Stauss M, Woywodt A (2022) Is open access a misnomer? Lancet 399:P1226. https://doi.org/10.1016/S0140-6736(22)00107-6
::::* [[Paywall journalism]]
=== Living and non-living communications ===
::::* The concept of ''[[Living Communications]]'' is not new. The most successful textbooks are updated by the original author(s) or successors who publish new versions as sequential editions. '''Biochemistry''' ([[Lehninger 1970 Worth Publishers |Lehninger 1970]]) continues as a classic textbook (Nelson DL, Cox MM. 2021. Lehninger Principles of Biochemistry. 8<sup>th</sup> ed.). '''Physical Chemistry''' - first published by Frederick Getman in 1913 entitled ''Outlines of Theoretical Chemistry'' - enjoyed a 5<sup>th</sup> edition in 1980 as the SI version of [[Alberty 1980 Physical chemistry |Alberty, Daniels F (1980)]], and in 2004 as the 4<sup>th</sup> edition of Silbey RJ, Alberty RA, Bawendi MG (2004). The textbooks are living communications which can be tracked as editions in their history of changing dates, authors, and even titles.
::::* The journal '''Bioenergetics Communications''' extends this established system of living communications in the form of sequential editions from textbooks and monographies to scientific publications in general. '''Editions''' of scientific publications are distinguished from '''versions''' of non-peer reviewed preprints.
::::* An interesting example of a non-living communication is a book entitled [[Van Liere 1963 Hypoxia |Hypoxia (1963)]] with an identical table of contents and largely identical text as [[Van Liere 1942 Anoxia |Anoxia (1942)]], mainly replacing the term ''anoxia'' by ''hypoxia''. 'Hypoxia' would appropriately be labelled as 2<sup>nd</sup> edition of 'Anoxia'.
=== Perhaps a 2<sup>nd</sup> edition ===
::::* ''The scientific literature is exploding in quantity even as it stands still in literary quality'' ([[Wells 2004 J Cell Biol |Wells 2004]]). - Sequential editions provide an opportunity to improve quality while preventing explosions on quantity.
::::* Footnote on p 757 ([[Wells 2004 J Cell Biol |Wells 2004]]): ''Some of the content of this article came from an earlier guide by R. Ward and K. LaMarco.'' - A PubMed search revealed no results on ''Ward R, LaMarco K'' (2022-02-04).
=== Definitions, standardization, training, and citation ===
::::* ''Full standardisation of definitions and analytical procedures could be feasible for new research efforts. .. For existing datasets and studies, harmonisation attempts to achieve some, but not necessarily perfect, homogeneity of definitions might need substantial effort and coordination. .. Large consortia and collaborations can allow the use of a common language among investigators for clinical definitions, laboratory measurements, and statistical analyses'' ([[Ioannidis 2014 Lancet]]).
::::* ''To avoid misinterpretation and dissemination of misinformation, the quality and appropriate citation of original sources of information are of paramount importance to science communication as regards open science'' ([[UNESCO 2021 Open Science]]).
::::* ''Clinical and laboratory researchers might also benefit from an opportunity to update their skills in view of newer methodological developments, perhaps through short courses and novel approaches to continued methodological education'' ([[Ioannidis 2014 Lancet]]).
::::* ''Encouraging international scientific collaborations, as one of the integral practices of open science and the most important driving factor for an intensive exchange of scientific knowledge and experience, as well as the paramount for the openness of science'' ([[UNESCO 2021 Open Science]]).
=== Reproducibility in biomedical research ===
::::* ''Over the recent years, there has been an increasing recognition of the weaknesses that pervade our current system of basic and preclinical research. This has been highlighted empirically in preclinical research by the inability to replicate the majority of findings presented in high-profile journals. The estimates for irreproducibility based on these empirical observations range from 75 % to 90 %. These estimates fit remarkably well with estimates of 85 % for the proportion of biomedical research that is wasted at-large'' ([[Begley 2015 Circ Res]]).
::::* ''The opportunity is to introduce, demand, and reward a level of rigor and robustness in designing, conducting, reporting, interpreting, validating, and disseminating research that is currently lacking from many areas of biomedical research'' ([[Begley 2015 Circ Res]]).
::::* ''In 2013, John Bohannon published the article 'Who's afraid of peer review?', which pointed to the core problem (13). He wrote a study in which he generated fake academic articles with a content devoid of scientific meaning and with obvious errors and omissions. This study was sent to more than 300 open-access journals, and more than 150 of them accepted it for publication with virtually no signs of quality control or peer review. Half of these journals were registered in the Directory of Open Access Journals (DOAJ), which is worrisome. The objective of this registry is to list quality-assured open-access journals to distinguish them from unscrupulous operators (so-called 'predatory journals') (14)'' ([[Hagve 2020 Tidsskr Nor Legeforen]]).
::::* ''Adopt preferred publication of negative over positive results; require very demanding reproducibility criteria before publishing positive results'' ([[Young 2008 PLoS Med]]).
::::* ''Scientific productivity cannot be judged simply by number of publications. Publication of many low-quality articles is worse than is production of none'' ([[Ioannidis 2014 Lancet]]).
::::* ''The delay between the reporting of an initial positive study and subsequent publication of concurrently performed but negative results is measured in years [10,11]'' ([[Young 2008 PLoS Med]]).
=== Further reading ===
:::: The following references are not quoted in the text but are relevant in an extended discussion of the topic.
|?Was published in year=Year
:: '''Further weblinks'''
::::* [[MitoPedia: BEC]] - [[Paywall journalism]]
::::* Leiden manifesto for research metrics - http://www.leidenmanifesto.org/
::::* The metric tide - https://responsiblemetrics.org/the-metric-tide/
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