MitoPedia: Gentle Science

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Bioenergetics Communications is the Open Access journal for publishing scientific and technical advances in bioenergetics and mitochondrial physiology in Living Communications Open Access logo.png

MitoPedia: Gentle Science

Bioenergetics Communications
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MitoPedia: Gentle Science

TermAbbreviationDescription
ASAPbioScience only progresses as quickly and efficiently as it is shared. But even with all of the technological capabilities available today, the process of publishing scientific work is taking longer than ever. ASAPbio (Accelerating Science and Publication in biology) is a scientist-driven nonprofit working to address this problem by promoting innovation and transparency in life sciences communication. In 2015, ASAPbio founder Ron Vale published an analysis of the increasing time to first-author publication among graduate students at UCSF, and proposed a more widespread use of preprints in the life sciences as a potential solution.
Advantage of preprintsThe advantages of preprints, the excitement and concerns about the role that preprints can play in disseminating research findings in the life sciences are discussed by N Bhalla (2016).
Bioenergetics Exhibition - Art meets Gentle Science
Ethics on publishingEthics on publishing follow COPE's guidelines (or equivalent). A journal's policy on publishing ethics should be clearly visible on its website, and should refer to: (1) Journal policies on authorship and contributorship; (2) How the journal will handle complaints and appeals; (3) Journal policies on conflicts of interest / competing interests; (4) Journal policies on data sharing and reproducibility; (5) Journal's policy on ethical oversight; (6) Journal's policy on intellectual property; and (7) Journal's options for post-publication discussions and corrections.
F1000ResearchF1000Research is an Open Research publishing platform for life scientists, offering immediate publication of articles and other research outputs without editorial bias. All articles benefit from transparent peer review and the inclusion of all source data. It is thus not a preprint server, but posters and slides can be published without author fees. Published posters and slides receive a DOI (digital object identifier) and become citable after a very basic check by our in-house editors.
Gentle Science
Living CommunicationsLCWith Living Communications, Bioenergetics Communications (BEC) is taking the next step from pre-print to re-print. Living Communications allow additions and corrections of a publication with Open Peer Review, such that the publication can evolve with full traceability, instead of remaining a static outdated paper. The concept of Living Communications persues a novel culture of scientific communication, addressing the conflict between long-term elaboration and validation of results and concepts, versus sharing quickly important preliminary and controversial contributions. Updated versions of Living Communications evolve on the basis of additions or corrections posted on the BEC website of the resource publication, until a new version is published. Evolution of a Living Communication is more resourceful and efficient than a ‘new’ publication. Living Communications provide a pathway along the scientific culture of lively debate towards tested and trusted milestones of research, from pre-print to re-print, from initial steps to next steps.
MitoFit Preprint ArchivesMitoFit Preprint ArchMitoFit Preprint Archives is an Open Access preprint server for mitochondrial physiology and bioenergetics.
MitoPedia: BEC
Open AccessOA
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Open Access (OA) academic articles comprise all different forms of published research that are distributed online, free of charge and with an open license to facilitate the distribution and reuse. The open access repositories serve as the perfect vehicle to transmit free knowledge, including but not limited to peer-reviewed and non-peer-reviewed academic journal articles, conference papers, theses, book chapters and monographs. Driven by the problems of social inequality caused by restricting access to academic research, the Open Access movement changes the funding system of published literature allowing for more readers and thus increased access to scientific knowledge, as well as addressing the economic challenges and unsustainability of academic publishing. In addition to being free to read (gratis), open access articles may also be free to use (libre) where the copyright is held by the authors and not the publisher.
PREreviewPREreview encourages scientists to post their scientific outputs as preprints. PREreview makes it easier to start and run a Preprint Journal Club, or integrate preprint review into conventional journal clubs. PREreview seeks to diversify peer review in the academic community by crowdsourcing pre-publication feedback to improve the quality of published scientific output, and to train early-career researchers (ECRs) in how to review others' scientific work. We want to facilitate a cultural shift in which every scientist posts, reads, and engages with preprints as standard practice in scholarly publishing. We see PREreview as a hub to support and nurture the growth of a community that openly exchanges timely, constructive feedback on emerging scientific outputs. We believe that by empowering ECRs through peer review training programs, thereby increasing the diversity of researchers involved in the peer review process, PREreview will help establish a healthier and more sustainable culture around research dissemination and evaluation. This project was born in April 2017 as a collaboration between Samantha Hindle and Daniela Saderi, scientists and ASAPbio Ambassadors, with help from Josh Nicholson, at the time working for Authorea.
PreprintA preprint is {Quote} a way in which a manuscript containing scientific results can be rapidly communicated from one scientist, or a group of scientists, to the entire scientific community {end of Quote}.
Quality Assurance
Reproducibility crisisAn experiment or study is reproducible or replicable when subsequent experiments confirm the results. This is re-search. However, we can define different types of reproducibility depending on the conditions that we use to replicate the previous work or in the information available. Our aim is to focus mostly on two different kinds1:

1. Direct: Is when we obtaining the same results using the same experimental conditions, materials, and methods as described in the original experiment. This would be the ideal reproducibility of an experiment however, it requires a very accurate description of how the original experiment was performed. Some journals are trying to resolve the reproducibility crisis improving the rigor and the excellence on the reported methods and results (e.g. STAR Methods in Cell Press).

2. Systematical: Refers to obtaining the same results, but under different conditions; for example, using another cell line or mouse strain, or inhibiting a gene pharmacologically instead of genetically. This open the door to subsequent studies to find the conditions under which an initial finding holds.


Gentle Science

References: Gentle Science

 Was published in yearHas title
National Academies of Sciences, Engineering, and Medicine 2020 Addressing the underrepresentation of women2020National Academies of Sciences, Engineering, and Medicine (2020) Promising practices for addressing the underrepresentation of women in science, engineering, and medicine: opening doors. The National Academies Press, Washington DC https://doi.org/10.17226/25585.
National Academies of Sciences, Engineering, and Medicine 2020 Advancing Open Science practices2020National Academies of Sciences, Engineering, and Medicine (2020) Advancing Open Science practices: stakeholder perspectives on incentives and disincentives. The National Academies Press, Washington DC https://doi.org/10.17226/25725.
National Academies of Sciences, Engineering, and Medicine 2018 Sexual harassment2018National Academies of Sciences, Engineering, and Medicine (2018) Sexual harassment of women: climate, culture, and consequences in academic sciences, engineering, and medicine. The National Academies Press, Washington DC. doi: https://doi.org/10.17226/24994.
Sansone 2018 bioRxiv2018Sansone SA, McQuilton P, Rocca-Serra P, Gonzalez-Beltran A, Izzo M, Lister A, Thurston M, Batista D, Granell R, Adekale M, Dauga D, Ganley E, Hodson S, Lawrence R, Khodiyar V, Tenenbaum J, Axton JM, Ball M, Besson S, Bloom T, Bonazzi V, Jimenez R, Carr D, Chan WM, Chung C, Clement-Stoneham G, Cousijn H, Dayalan S, Dumontier M, Yeumo ED, Edmunds S, Everitt N, Fripp D, Goble C, Golebiewski M, Hall N, Hanisch R, Hucka M, Huerta M, Kenall A, Kiley R, Klenk J, Koureas D, Larkin J, Lemberger T, Lynch N, Schriml L, Ma'ayan A, MacCallum C, Mons B, Moore J, Muller W, Murray H, Nobusada T, Noesgaard D, Paxton-Boyd J, Orchard S, Rustici G, Schurer S, Sharples K, Soares e Silva M, Stanford NJ, Subirats-Coll I, Swedlow J, Tong W, Wilkinson M, Wise J, Yilmaz P (2018) FAIRsharing, a cohesive community approach to the growth in standards, repositories and policies. bioRxiv 245183; doi: https://doi.org/10.1101/245183 .
Avasthi 2018 eLife2018Avasthi P, Soragni A, Bembenek JN (2018) Point of View: Journal clubs in the time of preprints. eLife 7:e38532.
Sarabipour​ 2018 PeerJ Preprints2018Sarabipour S, Debat HJ, Emmott E, Burgess S, Schwessinger B, Hensel Z (2018) On the value of preprints: an early career researcher perspective. PeerJ Preprints 6:e27400v1 https://doi.org/10.7287/peerj.preprints.27400v1.
National Academies of Sciences, Engineering, and Medicine 2018 Science data infrastructure2018National Academies of Sciences, Engineering, and Medicine (2018) International coordination for science data infrastructure: Proceedings of a workshop—in brief.. The National Academies Press, Washington DC doi: https://doi.org/10.17226/25015.
National Academies of Sciences, Engineering, and Medicine 2017 Fostering integrity in research2017The National Academies of Sciences, Engineering, and Medicine (2017) Fostering integrity in research. The National Academies Press, Washington, DC doi:https://doi.org/10.17226/21896.
Wasserstein 2016 The American Statistician2016Wasserstein RL, Lazar NA (2016) The ASA's statement on p-values: context, process, and purpose. The American Statistician 70:129-33.
Yordanov 2015 BMJ2015Yordanov Y, Dechartres A, Porcher R, Boutron I, Altman DG, Ravaud P (2015) Avoidable waste of research related to inadequate methods in clinical trials. BMJ 350:h809.
Horton 2015 Lancet2015Horton R (2015) Offline: What is medicine’s 5 sigma? Lancet 385:1380.
Begley 2015 Circ Res2015Begley CG, Ioannidis JP (2015) Reproducibility in science: improving the standard for basic and preclinical research. Circ Res 116:116-26.
Bilder 2015 Figshare2015Bilder G, Lin J, Neylon C (2015) Principles for open scholarly infrastructure-v1. Figshare: retrieved 2019-04-18 http://dx.doi.org/10.6084/m9.figshare.1314859.
Ioannidis 2014 Lancet2014Ioannidis JP, 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. Lancet 383:166-75.
Schatz 2013 Biochem Biophys Res Commun2013Schatz G (2013) Getting mitochondria to center stage. Biochem Biophys Res Commun 434:407-10.
Fortier 2010 Int J Epidemiol2010Fortier I, Burton PR, Robson PJ, Ferretti V, Little J, L'Heureux F, Deschênes M, Knoppers BM, Doiron D, Keers JC, Linksted P, Harris JR, Lachance G, Boileau C, Pedersen NL, Hamilton CM, Hveem K, Borugian MJ, Gallagher RP, McLaughlin J, Parker L, Potter JD, Gallacher J, Kaaks R, Liu B, Sprosen T, Vilain A, Atkinson SA, Rengifo A, Morton R, Metspalu A, Wichmann HE, Tremblay M, Chisholm RL, Garcia-Montero A, Hillege H, Litton JE, Palmer LJ, Perola M, Wolffenbuttel BH, Peltonen L, Hudson TJ (2010) Quality, quantity and harmony: the DataSHaPER approach to integrating data across bioclinical studies. Int J Epidemiol 39:1383-93.
Schatz 2007 Annu Rev Biochem2007Schatz G (2007) The magic garden. Annu Rev Biochem 76: 673-678.
Ioannidis 2005 PLoS Med2005Ioannidis JP (2005) Why most published research findings are false. PLoS Med 2005 Aug;2(8):e124.
Ernster 1981 J Cell Biol1981Ernster L, Schatz G (1981) Mitochondria: a historical review. J Cell Biol 91:227s-55s.
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