Gnaiger 2021 Bioenerg Commun

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Bioenergetics Communications        
Gnaiger 2020 BEC MitoPathways
       
Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1.
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Bioenergetics Communications
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Gnaiger E (2021) Beyond counting papers – a mission and vision for scientific publication. https://doi.org/10.26124/bec:2021-0005

» Bioenerg Commun 2021.5. Open Access pdf published online 2021-12-31

Gnaiger Erich (BEC 2021.5) Bioenerg Commun

Abstract: BEC.png doi:10.26124/bec:2021-0005

Graphical abstract

Launching and maintaining a scientific journal must be reflected and communicated with a message at a time of excessive numbers of research papers submitted to for-profit publishers of traditional paywall and predatory journals. Bioenergetics Communications BEC supports the UNESCO recommendation on Open Science and DORA. BEC introduces the concept of Living Communications to address the conflict between (R) rapid sharing of new methods and results, (E) efficient prevention of exponentially increasing numbers of publications, and (C) quality control as a time-demanding and expensive instrument to ensure reproducibility. Weekly or monthly printed issues are yesterday’s concept of prescription journals replaced by commonly and immediately accessible formats in the digital era of Open Access online publishing. The academic publishing ecosystem must be changed to re-allocate publication fees from publishers to science producers.

Keywords: authorship, consortia, inflation-attention crisis, living communication, open peer review, open science, publication, repeatability, reproducibility, teams, value-impact
Bioblast editor: Gnaiger E O2k-Network Lab: AT Innsbruck Oroboros

ORCID: ORCID.png Gnaiger E

Acknowledgements

Template NextGen-O2k.jpg
I thank Lisa Tindle-Solomon, Paolo Cocco, and Luiza Cardoso for their invaluable contributions in launching Bioenergetics Communications. Initial steps supported by Horizon 2020 project NextGen-O2k.


References and weblinks

LinkReferenceYearView
Arese Lucini F, Morone F, Tomassone MS, Makse HA (2021) Diversity increases the stability of ecosystems. PLOS ONE 15:e0228692. https://doi.org/10.1371/journal.pone.02286922021PMID: 32330134 Open Access
Begley CG, Ioannidis JPA (2015) Reproducibility in science: improving the standard for basic and preclinical research. Circ Res 116:116-26. https://doi.org/10.1161/CIRCRESAHA.114.3038192015PMID: 25552691 Open Access
Buranyi S (2017) Is the staggeringly profitable business of scientific publishing bad for science? Guardian 2017-06-27.2017Open Access
Cardoso LHD, Doerrier C, Gnaiger E (2021) Magnesium Green for fluorometric measurement of ATP production does not interfere with mitochondrial respiration. https://doi.org/10.26124/bec:2021-0001BEC 2021.1Bioenerg Commun 2021.1. BEC pdf published online 2021-06-30

Day S, Rennie S, Luo D, Tucker JD (2020) Open to the public: paywalls and the public rationale for open access medical research publishing. Res Involv Engagem 6:8. https://doi.org/10.1186/s40900-020-0182-y2020PMID: 32161664 Open Access
Gnaiger E (2001) Bioenergetics at low oxygen: dependence of respiration and phosphorylation on oxygen and adenosine diphosphate supply. https://doi.org/10.1016/S0034-5687(01)00307-32001Bioblast pdf
Respir Physiol 128:277-97. PMID: 11718759
Gnaiger E (2019) Editorial: A vision on preprints for mitochondrial physiology and bioenergetics. https://doi.org/10.26124/mitofit:190002.v22019-04-24MitoFit Preprint Arch 2019.2.v2.
MitoFit pdf
Editorial: A vision on preprints



Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. https://doi.org/10.26124/bec:2020-0002BEC 2020.2Bioenerg Commun 2020.2. Open Access pdf published online 2020-12-30

Gnaiger E et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. https://doi.org/10.26124/bec:2020-0001.v1BEC 2020.1Bioenerg Commun 2020.1. Open Access pdf published online 2020-05-20

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S (2010) A draft sequence of the Neandertal genome. Science 328:710-22. doi: 10.1126/science.11880212010PMID: 20448178 Open Access
Hagve M (2020) The money behind academic publishing. Tidsskr Nor Legeforen doi: 10.4045/tidsskr.20.0118.2020Open Access
Ioannidis JPA, Greenland S, Hlatky MA, Khoury MJ, Macleod MR, Moher D, Schulz KF, Tibshirani R (2014) Increasing value and reducing waste in research design, conduct, and analysis. https://doi.org/10.1016/S0140-6736(13)62227-82014Lancet 383:166-75. PMID: 25552691 Open Access
Komlódi T, Cardoso LHD, Doerrier C, Moore AL, Rich PR, Gnaiger E (2021) Coupling and pathway control of coenzyme Q redox state and respiration in isolated mitochondria. https://doi.org/10.26124/bec:2021-0003BEC 2021.3Bioenerg Commun 2021.3. Open Access pdf published online 2021-11-11

Komlódi T, Sobotka O, Gnaiger E (2021) Facts and artefacts on the oxygen dependence of hydrogen peroxide production using Amplex UltraRed. https://doi.org/10.26124/bec:2021-0004BEC 2021.4Bioenerg Commun 2021.4. Open Access pdf published online 2021-12-21

Krako Jakovljevic N, Ebanks B, Katyal G, Chakrabarti L, Markovic I, Moisoi N (2021) Mitochondrial homeostasis in cellular models of Parkinson’s Disease. https://doi.org/10.26124/bec:2021-0002BEC 2021.2Bioenerg Commun 2021.2. Open Access pdf published online 2021-Oct-06

Marshall McLuhan Herbert, Fiore Quentin (1967) The Medium is the Massage. Penguin Books 160 pp.1967
Pääbo S (2014) Neanderthal man. In search of lost genomes. Basic Books, New York:275 pp.2014Wikipedia
youtube
Triggle Chris R, Triggle David J (2017) From Gutenberg to Open Science: an unfulfilled odyssey. Drug Dev Res 78:3-23.2017PMC5324562 Open Access
UNESCO (2021) Draft recommendation on Open Science. UNESCO 41 C/22. https://unesdoc.unesco.org/ark:/48223/pf00003788412021Open Access
Wieser W, Ott J, Schiemer F, Gnaiger E (1974) An ecophysiological study of some meiofauna species inhabiting a sandy beach at Bermuda. Mar Biol 26:235-48.1974Springer
Young NS, Ioannidis JPA, Al-Ubaydli O (2008) Why current publication practices may distort science. PLoS Med 5:e201. doi: 10.1371/journal.pmed.00502012008PMID: 18844432 Open Access
Weblinks


Living Communication

Last update 2022-02-04

Publication and registration into oblivion

2021-01-01
  • 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).
  • 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

2022-01-04
  • 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

2022-01-02
  • 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 (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 [9], 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 [38] (Day 2020 Res Involv Engagem).
  • 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?

2022-03-25

Living and non-living communications

2022-01-17
  • 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) continues as a classic textbook (Nelson DL, Cox MM. 2021. Lehninger Principles of Biochemistry. 8th ed.). Physical Chemistry - first published by Frederick Getman in 1913 entitled Outlines of Theoretical Chemistry - enjoyed a 5th edition in 1980 as the SI version of Alberty, Daniels F (1980), and in 2004 as the 4th 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 Hypoxia (1963) with an identical table of contents and largely identical text as Anoxia (1942), mainly replacing the term anoxia by hypoxia. 'Hypoxia' would appropriately be labelled as 2nd edition of 'Anoxia'.

Perhaps a 2nd edition

2022-02-04
  • The scientific literature is exploding in quantity even as it stands still in literary quality (Wells 2004). - Sequential editions provide an opportunity to improve quality while preventing explosions on quantity.
  • Footnote on p 757 (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

2022-01-02
  • 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

2022-01-04
  • 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.
LinkReferenceYearView
Amaral OB, Neves K (2021) Reproducibility: expect less of the scientific paper. Nature 597:329-31. https://doi.org/10.1038/d41586-021-02486-72021PMID: 34526702 Open Access
Baker M (2016) 1,500 scientists lift the lid on reproducibility. Nature 533:452-4.2016PMID: 27225100 Open Access
Besançon L, Peiffer-Smadja N, Segalas C, Jiang H, Masuzzo P, Smout C, Billy E, Deforet M, Leyrat C (2021) Open science saves lives: lessons from the COVID-19 pandemic. BMC Med Res Methodol 21:117. doi: 10.1186/s12874-021-01304-y2021PMID: 34090351 Open Access
Besançon L, Rönnberg N, Löwgren J, Tennant JP, Cooper M (2020) Open up: a survey on open and non-anonymized peer reviewing. Res Integr Peer Rev 5:8. doi: 10.1186/s41073-020-00094-z2020PMID: 32607252 Open Access
Carpenter CR, Cone DC, Sarli CC (2014) Using publication metrics to highlight academic productivity and research impact. Acad Emerg Med 21:1160-72.2014PMID: 25308141 Open Access
Fox CW (2021) Which peer reviewers voluntarily reveal their identity to authors? Insights into the consequences of open-identities peer review. Proc Biol Sci 288(1961):20211399. doi: 10.1098/rspb.2021.13992021PMID: 34702079 Open Access
Ioannidis JPA (2005) Why most published research findings are false. PLoS Med 2005 Aug;2(8):e124.2005PMID: 16060722 Open Access
Kelly AR, Autry MK (2013) Access, accommodation, and science: knowledge in an “open” world. First Monday 18. https://doi.org/10.5210/fm.v18i6.4341.2013Open Access
Rodgers P, Collings A (2021) What have we learned? Elife 10:e75830. doi: 10.7554/eLife.758302021PMID: 34874010 Open Access
Ross-Hellauer T (2017) What is open peer review? A systematic review. F1000Res 6:588. doi: 10.12688/f1000research.11369.22017PMID: 28580134 Open Access
Ross-Hellauer T, Görögh E (2019) Guidelines for open peer review implementation. Res Integr Peer Rev 4:4. doi: 10.1186/s41073-019-0063-92019PMID: 30858990 Open Access
Van Noorden R (2013) Open access: the true cost of science publishing. Nature 495:426–9.2013Nature Open Access
Wells WA (2004) Me write pretty one day: how to write a good scientific paper. J Cell Biol 165:757-8. doi: 10.1083/jcb.200403137.2004PMID: 15210725 Open Access
Further weblinks


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