MitoPedia: BEC

From Bioblast
Jump to navigation Jump to search


Bioenergetics Communications        
Gnaiger 2020 BEC MitoPathways
       
Gnaiger Erich et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. Bioenerg Commun 2020.1.
        MitoPedia: BEC         MitoPedia: Gentle Science         MitoFit Preprints         DOI Data Center
Bioenergetics Communications is the Open Science journal on bioenergetics and mitochondrial physiology with Living Communications Open Access logo.png - ISSN 2791-4690

MitoPedia: BEC

Bioenergetics Communications
Template NextGen-O2k.jpg
MitoPedia     Terms and abbreviations     Preprints and history     MiP and biochemistry     Concepts and methods     MitoPedia: SUIT     MitoPedia: O2k




MitoPedia

MitoPedia: Bioenergetics Communications

TermAbbreviationDescription
Allegations of research misconductAllegations of research misconduct are handled with care. Publishers and editors shall take reasonable steps to identify and prevent the publication of papers where research misconduct has occurred, including plagiarism, citation manipulation, and data falsification/fabrication, among others. In no case shall a journal or its editors encourage such misconduct, or knowingly allow such misconduct to take place. In the event that a journal's publisher or editors are made aware of any allegation of research misconduct relating to a published article in their journal, the publisher or editor shall follow COPE's guidelines (or equivalent) in dealing with allegations.
BEC 2020.1 doi10.26124bec2020-0001.v1
BEC authors
BEC editors
BEC formats
BEC reviewers
Bioenerg Commun
Bioenergetics Communications Policies
Biomedical sentence similarity
COPE core practices for researchCOPE core practices for research are applicable to all involved in publishing scholarly literature. »COPE's guidelines.
Comma for separating a term and its abbreviation,Should we used a comma for separating a term and its abbreviation in the text? The SI Brochure frequently does not use a comma. The comma might be added, if it helps to clarify the distinction between the term and its abbreviation. The example “reduced Q fraction, Qr” – the sequence of Q and Qr may be confusing without comma. There will always be examples, where it is not clear, if a comma is needed.
CopyrightAuthors retain the copyright for the contents of their manuscripts published in Bioenergetics Communications. {Quote} All preprints are posted with a Creative Commons CC BY 4.0 license, ensuring that authors retain copyright and receive credit for their work, while allowing anyone to read and reuse their work. {end of Quote}
Creative Commons Attribution LicenseOpen Access preprints (not peer-reviewed) and articles (peer-reviewed) distributed under the terms of the Creative Commons Attribution License allow unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited. © remains with the authors, who have granted the publisher license in perpetuity.
DORADORA
Dorabadge5.png
The Declaration on Research Assessment DORA recognizes the need to improve the ways in which researchers and the outputs of scholarly research are evaluated.
DataCiteDataCiteDataCite is a global community of organizations and researchers identifying and citing research outputs and resources. We provide services to create persistent records of research, enable discovery and reuse, and support workflows throughout the research lifecycle.
Decimal marker and spaces between groups of numerals.A decimal marker is used to separate the integral part of numbers from the decimal part. The SI recommends: "the symbol for the decimal marker shall be either the point on the line or the comma on the line". In English language versions, the dot (point on the line) should be used uniquely as the decimal marker. To avoid ambiguities, BEC follows the SI recommendation that “Numbers may be divided in groups of three in order to facilitate reading; neither dots nor commas are ever inserted in the spaces between groups” (pages 183-184).
Digital Object IdentifierDOIA Digital Object Identifier, DOI, is a persistent identifier used to uniquely identify online publications in order to ensure they remain traceable, searchable and citable over the long term. Compared to other types of persistent identifiers, the DOI system is widespread and well established in the life sciences arena, and it provides widely accepted visible proof that a publication is citable.
Directory of Open Access JournalsDOAJThe Directory of Open Access Journals is a free online directory that indexes and provides access to open access peer-reviewed journals.
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.
File:MitoFitPreprints and BEC manuscript template.docxBioenergetics Communications and MitoFit Preprints manuscript template.
Gentle Science
Gnaiger 2020 BEC MitoPathways
HyphenationHyphenation is used to connect two words (compound words) or two parts of a word to clarify the meaning of a sentence. The same two words may be hyphenated or not depending on context. Hyphenation may present a problem when searching for a term such as 'Steady state'. It is helpful to write 'steady-state measurement', to clarify that the measurement is performed at steady state, rather than implying that a state measurement is steady. But this does not imply that hyphenation is applied to the 'measurement performed at steady state'. Thus, the key word is 'steady state'. Compound adjectives should be hyphenated (steady-state measurement), but if the compound adjective follows the term (measurement at steady state), hyphenation does not add any information and should be avoided. Find more examples and guidelines in the grammarly blog on Hyphen and in apastyle.apa.org.
Impact factorIFImpact factor is a measure of a scientific journal's citations per publication. The Journal Citation Reports, maintained by Clarivate Analytics, provides the calculated impact factors. The IF is frequently used as an indicator of a journal's importance or prestige, which is nowadays increasingly contested.
International Standard Serial NumberISSNThe International Standard Serial Number, ISSN, is a code used to identify periodical publications, independent of which media are used (print and/or electronic). - Bioenergetics Communications, BEC: ISSN 2791-4690
Journal indexingJournal indexing allows publications to be found on search tools/databases. Each database might have different criteria of inclusion.
Journal issueAn issue of a journal or periodical is a number, which typically indicates how many times a volume of the journal has been published in sequence.
Journal volumeThe volume of a journal or periodical is a number, which in many cases indicates the sequential number of years the journal has been published. Alternatively, the volume number may indicate the current year, independent of the year in which the journal published its first volume. A volume may be subdivided into issues.
Keywords-MitoPedia in BECKeywords—MitoPedia is the concept to link keywords in articles published in Bioenergetics Communications (BEC) to MitoPedia terms. Authors should consider the message in the selected keywords. Provide consistent definitions of your keywords by linking them to MitoPedia. Extend MitoPedia entries critically by your contributions. The BEC editorial team will hyperlink your keywords with MitoPedia, and a reference to your BEC publication will be generated automatically from the MitoPedia term to your publication. With your contributions, BEC elevates keywords to terms with meaning. Your article gains visibility.
Living CommunicationsLCWith Living Communications, Bioenergetics Communications (BEC) takes the next step from pre-print to re-print. The concept of Living Communications pursues a novel culture of scientific communication, addressing the conflict between long-term elaboration and validation of results versus sharing without delay improved methods and preliminary findings. Following the preprint concept, updates may be posted on the BEC website of the resource publication. Updated versions of Living Communications are submitted for Open Peer Review with full traceability. In contrast to static papers, evolution of Living Communications 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.
Manuscript template for MitoFit PreprintsManuscripts template for MitoFit Preprints and Bioenergetics Communications.
MitoFit PreprintsMitoFit Prep
MitoFit Preprints.png
MitoFit Preprints is an Open Access preprint server for mitochondrial physiology and bioenergetics.
MitoPedia: Gentle Science
Open AccessOA
Open Access logo.png
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. Definition by the Directory of Open Access Journals (DOAJ): "We define these as journals where the copyright holder of a scholarly work grants usage rights to others using an open license (Creative Commons or equivalent) allowing for immediate free access to the work and permitting any user to read, download, copy, distribute, print, search, or link to the full texts of articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose."
Open ScienceOS
Open Access logo.png
Building on the essential principles of academic freedom, research integrity and scientific excellence, open science sets a new paradigm that integrates into the scientific enterprise practices for reproducibility, transparency, sharing and collaboration resulting from the increased opening of scientific contents, tools and processes. Open science is defined as an inclusive construct that combines various movements and practices aiming to make multilingual scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation and communication to societal actors beyond the traditional scientific community. It comprises all scientific disciplines and aspects of scholarly practices, including basic and applied sciences, natural and social sciences and the humanities, and it builds on the following key pillars: open scientific knowledge, open science infrastructures, science communication, open engagement of societal actors and open dialogue with other knowledge systems.
Paywall journalismThough often defined from the individual reader's perspective, a paywall can also apply to an institution (such as a library) or the author. Paywall journalism is the opposite of Open Access. Open Science does not accept paywalls with the argument, that the public pays for governmentally funded research, hence research funded by public grants should be published with open access for the public without paywalls. Paywalls are most frequently defined from the perspective of the individual reader, who has to pay for an article or pay a journal subscription as a requisite for obtaining full access to the information that is otherwise hidden behind the paywall (reader-paywall journal). From the perspective of the authors, however, an author-paywall journal is defined as any journal which requests publication charges or page charges from the authors for publishing the manuscript Open Access or publishing it at all. Similarly, an institutional-paywall journal charges an institution – typically university libraries – for granting open access to the members of this institution. As long as paywall journalism prevails in science, at least paywall transparence should be required, to declare for each publication not only the reader-paywall costs but provide the full information on the author-paywall and institutional-paywall expenses.
Plan SSPlan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. According to Science Europe, "Plan S requires that recipients of research funding from cOAlition S organisations make the resulting publications available immediately (without embargoes) and under open licences, either in quality Open Access platforms or journals or through immediate deposit in open repositories that fulfil the necessary conditions."
PubMedPubMed is a free search tool for articles in the life sciences field.
Publication efficiencyFr,a/pPublication efficiency is the fraction Fr,a/p of reproducible publications Nr which are among the number Na of publications that receive attention and meaningful interpretation, per total count Np of all published communications. Publication efficiency Fr,a/p = Fr/p·Fa/p is low due to (1) the reproducibility crisis expressed as low reproducibility efficiency Fr/p = Nr/Np, and (2) the inflation crisis expressed as low attention efficiency Fa/p = Na/Np. Estimates of these partial efficiencies vary from field to field. With Fr/p=0.15 and Fa/p=0.05, the current publication efficiency is as low as 0.0075, or only 0.75 % of all presently published communictions are reproducible and receive attention and meaningful interpretation. Reduction of the number of irreproducible zero-value publications is the most effective measure to reduce the paper mass excess (PME) in the reproducibility-inflation (R&I)-crisis. Several regulatory mechanisms for improvement are practically ignored although theoretically available.
Quantities, symbols, and unitsIn the context of quantities, symbols, and units, a code is required to convert terms defining physicochemical quantities into symbols (encoding) and to decode symbols as used in equations, text, and figures. Then symbols and abbreviations gain meaning. Simple symbols — such as Q or N — are used with different meanings depending on context (think of Q for heat and Q for electric charge; or N for number of cells and N for number of O2 molecules). The context provides the code. When the context is extended, the symbols have to be expanded too, including more detail to avoid confusion (Qth versus Qel; Nce versus NO2). Then symbols may appear too complicated, loosing the function of sending their message quickly. There is no single best way to design the right symbol or to replace meaningful symbols (Qel) by ambiguous abbreviations (Q) — all depends on context. We need to use the adequate medium (words, symbols, and abbreviations; equations, text, and figures; videos and slide presentations) and provide the code to achieve communication. The medium is the message, the message is the meaning — from Marshall McLuhan to Hofstadter.
References in BEC https-formatBEC https-formatReferences in BEC https-format show (1) the list of authors, (2) the year of publication in parentheses, (3) the title of the publication, and (4) the https://doi.org/ link. Removing all the unnecessary detail of journal name and pages, the focus is on authors, year, and title of the reference, which is a concept in line with DORA. The https-link then does the full job. In exceptional cases when there is no such link, the following formats would apply: a https://pubmed.ncbi.nlm.nih.gov/ link, a link directly to an Open Access pdf, or the old conventional format for the reference. Scientific journals apply yesterday's concepts in the various formats of references with bewildering abbreviations of journals, volumes, issues, page numbers. We can do today's job much better using the BEC https-format:

  1. Arese Lucini F, Morone F, Tomassone MS, Makse HA (2021) Diversity increases the stability of ecosystems. https://doi.org/10.1371/journal.pone.0228692
  2. Begley CG, Ioannidis JPA (2015) Reproducibility in science: improving the standard for basic and preclinical research. https://doi.org/10.1161/CIRCRESAHA.114.303819.
  3. Buranyi S (2017) Is the staggeringly profitable business of scientific publishing bad for science? https://www.theguardian.com/science/2017/jun/27/profitable-business-scientific-publishing-bad-for-science
  4. 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:2021-0001
  5. Day S, Rennie S, Luo D, Tucker JD (2020) Open to the public: paywalls and the public rationale for open access medical research publishing. https://doi.org/10.1186/s40900-020-0182-y
  6. 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)00307-3
  7. ….

Compare with a conventional reference format in: Gnaiger E (2021) Beyond counting papers – a mission and vision for scientific publication. https://doi.org/10.26124/bec:2021-0005
SI prefixesThere are 20 SI prefixes defined to represent multiples and submiltiples of SI units.
Science - the conceptScienceAs per the 2017 UNESCO Recommendation on Science and Scientific Researchers, the term ‘science’ signifies the enterprise whereby humankind, acting individually or in small or large groups, makes an organized attempt, in cooperation and in competition, by means of the objective study of observed phenomena and its validation through sharing of findings and data and through peer review, to discover and master the chain of causalities, relations or interactions; brings together in a coordinated form subsystems of knowledge by means of systematic reflection and conceptualization; and thereby furnishes itself with the opportunity of using, to its own advantage, understanding of the processes and phenomena occurring in nature and society.
Science Citation IndexSCIThe Science Citation Index SCI offers bibliographical access to a curated collection of journals across 178 scientific disciplines. The SCI provides gold-standard lists of established journals.
ZenodoScience Europe: "Zenodo is an open source and free repository for storing data, code, materials, and any research artefact. It was created by CERN and launched within the frame of the OpenAIRE project, commissioned by the European Commission. It aims at fostering free and easy access to scientific results, scientific data, software, and publications to all researchers."
Bioenergetics Communications

References: Bioenergetics Communications

 Was published in yearHas title
Baglivo 2022 BECBEC 2022.8Baglivo E, Cardoso LHD, Cecatto C, Gnaiger E (2022) Statistical analysis of instrumental reproducibility as internal quality control in high-resolution respirometry. Bioenerg Commun 2022.8. https://doi.org/10.26124/bec:2022-0008
Serna 2022 BECBEC 2022.7Serna JDC, Ramos VM, Cabral-Costa JV, Vilas-Boas EA, Amaral AG, Ohya G, da Silva CCC, Kowaltowski AJ (2022) Measuring mitochondrial Ca2+ efflux in isolated mitochondria and permeabilized cells. https://doi.org/10.26124/bec:2022-0007
Heichler 2022 BECBEC 2022.6Heichler C, Nagy M, Wolf P (2022) Evaluation of hepatotoxic effects of acetaminophen on HepG2 cells by parallel real-time monitoring in a multi-sensor analysis platform for automated cell-based assays. https://doi.org/10.26124/bec:2022-0006
Balbaisi 2022 BECBEC 2022.5Balbaisi A, Stiban J (2022) Barth syndrome: a genetic ailment with a lipid component and bioenergetic ramifications. https://doi.org/10.26124/bec:2022-0005
Aasander Frostner 2022 BECBEC 2022.4Åsander Frostner E, Simón Serrano S, Chamkha I, Donnelly E, Elmér E, Hansson MJ (2022) Towards a treatment for mitochondrial disease: current compounds in clinical development. https://doi.org/10.26124/bec:2022-0004
Abed Rabbo 2022 BECBEC 2022.3Abed Rabbo M, Stiban J (2022) NUBPL: a mitochondrial Complex I deficiency disorder. https://doi.org/10.26124/bec:2022-0003
Heimler 2022 BECBEC 2022.2Heimler SR, Phang HJ, Bergstrom J, Mahapatra G, Dozier S, Gnaiger E, Molina AJA (2022) Platelet bioenergetics are associated with resting metabolic rate and exercise capacity in older adult women. https://doi.org/10.26124/bec:2022-0002
Gnaiger 2022.1 Bioenerg CommunBEC 2022.1Gnaiger E, Cardoso LHD, Tindle-Solomon L, Cocco P, eds (2022) Bioblast 2022: BEC inaugural conference. https://doi.org/10.26124/bec:2022-0001
Gnaiger 2021 Bioenerg CommunBEC 2021.5Gnaiger E (2021) Beyond counting papers – a mission and vision for scientific publication. https://doi.org/10.26124/bec:2021-0005
Gnaiger 2020 BEC MitoPathwaysBEC 2020.2Gnaiger E (2020) Mitochondrial pathways and respiratory control. An introduction to OXPHOS analysis. 5th ed. https://doi.org/10.26124/bec:2020-0002
BEC 2020.1 doi10.26124bec2020-0001.v1BEC 2020.1Gnaiger E et al ― MitoEAGLE Task Group (2020) Mitochondrial physiology. https://doi.org/10.26124/bec:2020-0001.v1
Floyd 2022 Lancet2022Floyd L, Stauss M, Woywodt A (2022) Is open access a misnomer? Lancet 399:P1226. https://doi.org/10.1016/S0140-6736(22)00107-6
UNESCO 2021 Open Science2021UNESCO (2021) Draft recommendation on Open Science. UNESCO 41 C/22. https://unesdoc.unesco.org/ark:/48223/pf0000378841
Day 2020 Res Involv Engagem2020Day 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-y
Taichman 2020 N Engl J Med2020Taichman DB, Backus J, Baethge C, Bauchner H, Flanagin A, Florenzano F, Frizelle FA, Godlee F, Gollogly L, Haileamlak A, Hong ST, Horton R, James A, Laine C, Miller PW, Pinborg A, Rubin EJ, Sahni P (2020) A disclosure form for work submitted to medical journals - a proposal from the International Committee of Medical Journal Editors. N Engl J Med 382:667-8. doi: 10.1056/NEJMe2000647
Besancon 2020 Res Integr Peer Rev2020Besançon 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-z
Gnaiger 2019 MitoFit Preprints Editorial2019-04-24Gnaiger E (2019) Editorial: A vision on preprints for mitochondrial physiology and bioenergetics. https://doi.org/10.26124/mitofit:190002.v2
Ross-Hellauer 2019 Res Integr Peer Rev2019Ross-Hellauer T, Görögh E (2019) Guidelines for open peer review implementation. Res Integr Peer Rev 4:4. doi: 10.1186/s41073-019-0063-9
Ross-Hellauer 2017 F1000Res2017Ross-Hellauer T (2017) What is open peer review? A systematic review. F1000Res 6:588. doi: 10.12688/f1000research.11369.2
Triggle 2017 Drug Dev Res2017Triggle Chris R, Triggle David J (2017) From Gutenberg to Open Science: an unfulfilled odyssey. Drug Dev Res 78:3-23.
Begley 2015 Circ Res2015Begley 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.114.303819
Ioannidis 2014 Lancet2014Ioannidis 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)62227-8
Young 2008 PLoS Med2008Young NS, Ioannidis JPA, Al-Ubaydli O (2008) Why current publication practices may distort science. PLoS Med 5:e201. doi: 10.1371/journal.pmed.0050201
Ioannidis 2005 PLoS Med2005Ioannidis JPA (2005) Why most published research findings are false. PLoS Med 2005 Aug;2(8):e124.
Bioenergetics Communications

MitoPedia topics: Preprints, Gentle Science