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Preprints in the Spotlight: Establishing Best Practices, Building Trust 1
ISSUE BRIEF Preprints in the Spotlight Establishing Best Practices, Building Trust May 27, 2020 Oya Y. Rieger Ithaka S+R provides research and Copyright 2020 ITHAKA. This work is strategic guidance to help the licensed under a Creative Commons Attribution-NonCommercial 4.0 academic and cultural communities International License. To view a copy of serve the public good and navigate the license, please see http://creative- economic, demographic, and commons.org/licenses/by-nc/4.0/. technological change. Ithaka S+R is ITHAKA is interested in disseminating part of ITHAKA, a not-for-profit this brief as widely as possible. Please organization that works to advance contact us with any questions about using and preserve knowledge and to the report: [email protected]. improve teaching and learning through the use of digital technologies. Artstor, JSTOR, and Portico are also part of ITHAKA. PREPRINTS IN THE SPOTLIGHT: ESTABLISHING BEST PRACTICES, BUILDING TRUST 1 Introduction Preprints have been getting a lot of attention recently. The COVID-19 pandemic—the first major health crisis since medical and biomedical preprints have become widely available online—has further underscored the importance of speedy dissemination of research outcomes. Preprints allow researchers to share results with speed, but raise questions about accuracy, misconduct, and our reliance on the “self-correcting” nature of the scientific enterprise. As scientists and health care professionals, as well as the general public, look for information about the pandemic, preprint services are growing in importance. So too are the policy decisions preprint platform leaders make. Even before the crisis struck, it was clear that 2020 would be a year of reckoning for preprints. -
Consistent Variations in Personality Traits and Their Potential for Genetic Improvement in The
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.21.257881. this version posted August 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Consistent variations in personality traits and their potential for genetic improvement in the 2 biocontrol agent Trichogramma evanescens 3 4 Silène Lartiguea,b,c, Myriam Yalaouib, Jean Belliardb, Claire Caravelb, Louise Jeandrozb, 5 Géraldine Groussierb, Vincent Calcagnob, Philippe Louâprec, François-Xavier Dechaume- 6 Moncharmontd, Thibaut Malausab and Jérôme Moreauc, e 7 8 a ENGREF AgroParisTech, Paris, France 9 10 b UMR Institut Sophia Agrobiotech, INRAE, UCA, CNRS, 06903 Sophia Antipolis, France 11 12 c UMR CNRS 6282 Biogéosciences, Université Bourgogne Franche-Comté, 6 Boulevard 13 Gabriel, 21000 Dijon, France 14 15 d Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, 69622 16 Villeurbanne, France 17 18 e Centre d'Études Biologiques de Chizé, UMR 7372, CNRS & La Rochelle Université, 79360 19 Villiers-en-bois, France 20 21 * Corresponding author: S. Lartigue, UMR Institut Sophia Agrobiotech, INRAE, UCA, 22 CNRS, Sophia Antipolis, France. E-mail address: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.21.257881. this version posted August 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Abstract 24 Improvements in the biological control of agricultural pests require improvements in the 25 phenotyping methods used by practitioners to select efficient biological control agent (BCA) 26 populations in industrial rearing or field conditions. -
Superresolution Microscopy of the Β-Carboxysome Reveals a Homogeneous Matrix
Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Niederhuber, Matthew J., Talley J. Lambert, Clarence Yapp, Pamela A. Silver, and Jessica K. Polka. 2017. “Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix.” Molecular Biology of the Cell 28 (20): 2734-2745. doi:10.1091/ mbc.E17-01-0069. http://dx.doi.org/10.1091/mbc.E17-01-0069. Published Version doi:10.1091/mbc.E17-01-0069 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:34651752 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA M BoC | ARTICLE Superresolution microscopy of the β-carboxysome reveals a homogeneous matrix Matthew J. Niederhubera,b,†, Talley J. Lambertc, Clarence Yappd, Pamela A. Silvera,b, and Jessica K. Polkaa,b,* aDepartment of Systems Biology, cDepartment of Cell Biology, and dImage and Data Analysis Core, Harvard Medical School, Boston, MA 02115; bWyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 ABSTRACT Carbon fixation in cyanobacteria makes a major contribution to the global carbon Monitoring Editor cycle. The cyanobacterial carboxysome is a proteinaceous microcompartment that protects Benjamin S. Glick and concentrates the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygen- University of Chicago ase (RuBisCO) in a paracrystalline lattice, making it possible for these organisms to fix CO2 Received: Jan 30, 2017 from the atmosphere. -
Downloads Presented on the Abstract Page
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. A systematic examination of preprint platforms for use in the medical and biomedical sciences setting Jamie J Kirkham1*, Naomi Penfold2, Fiona Murphy3, Isabelle Boutron4, John PA Ioannidis5, Jessica K Polka2, David Moher6,7 1Centre for Biostatistics, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom. 2ASAPbio, San Francisco, CA, USA. 3Murphy Mitchell Consulting Ltd. 4Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), Inserm, Paris, F-75004 France. 5Meta-Research Innovation Center at Stanford (METRICS) and Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, Stanford University, Stanford, CA, USA. 6Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Canada. 7School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada. *Corresponding Author: Professor Jamie Kirkham Centre for Biostatistics Faculty of Biology, Medicine and Health The University of Manchester Jean McFarlane Building Oxford Road Manchester, M13 9PL, UK Email: [email protected] Tel: +44 (0)161 275 1135 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Opening up Peer-Review Policies
FEATURE Opening Up Peer-Review Policies Jessica Polka, Tony Ross-Hellauer, and Gary McDowell Authors in many disciplines favor1 peer review moving out of the shadows and becoming a more transparent practice. Accordingly, platforms and publishers are increasingly implementing open peer review (OPR) to enable new kinds of discourse within the publishing process. Yet, these systems differ in what is revealed when and to whom. OPR can operate on many different parts of the review process. It can infl uence the process of peer review (who can comment on the manuscript, and whether they can communicate with one another) as well as the transparency of information about peer review (the visibility of the manuscript or reviewer names, reports), and it can operate at Photo by Javier Allegue Barros (https://unsplash.com/photos/ many different times, from before submission (i.e., preprints) C7B-ExXpOIE?utm_source=unsplash&utm_medium=referral&utm_ to after publication (i.e., post-publication commenting). One content=creditCopyText) on Unsplash. of us undertook a systematic analysis2 of defi nitions of OPR; this uncovered 7 core traits, which were used in 22 distinct Scholarly activity in open peer review has also made confi gurations. The most frequently used elements of OPR signifi cant progress. In January 2019, results were released were revealing reviewer identities (open identities) and from a trial in which 5 Elsevier journals6 began publishing all publishing reviews (open reports). peer reviews. It showed that each journals’ submission rates increased during the trial. While the rate at which reviewers Growth in open peer-review accepted invitations to review declined, these declines implementations and experiments matched global trends, so may not have been caused by the While open peer review has been practiced by publishers review model. -
Joint Species Distributions Reveal the Combined Effects of Host Plants, Abiotic Factors and Species Competition As Drivers of Species Abundances in Fruit Flies
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.07.414326; this version posted April 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. RESEARCH ARTICLE Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of species abundances in fruit flies Benoit Facon1,*, Abir Hafsi2,*, Maud Charlery de la Masselière2, 3 4 5 3 Stéphane Robin , François Massol , Maxime Dubart , Julien Chiquet , Enric Frago6, Frédéric Chiroleu2, Pierre-François Duyck2,7 & Virginie Ravigné2 1 Cite as: Facon B, Hafsi A, Charlery de INRAE, UMR PVBMT, F-97410 Saint Pierre, France la Masselière M, Robin S, Massol F, 2 CIRAD, UMR PVBMT, F-97410 Saint Pierre, France Dubart M, Chiquet J, Frago E, 3 Chiroleu F, Duyck P-F, Ravigné V Laboratoire MMIP – UMR INRA 518/AgroParisTech, Paris, France (2021) Joint species distributions 4 Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL reveal the combined effects of host - Center for Infection and Immunity of Lille, F-59000 Lille, France plants, abiotic factors and species 5 competition as drivers of community Univ. Lille, CNRS, UMR 8198 – Evo-Eco-Paleo, F-59000 Lille, France structure in fruit flies. bioRxiv, 6 CIRAD, UMR CBGP, France 2020.12.07.414326. ver. 4 peer- 7 reviewed and recommended by Peer IAC, Equipe ARBOREAL, BP 98857, Nouméa, Nouvelle-Calédonie community in Ecology. -
Accelerating Scientific Publication
Accelerating scientific publication Thierry Galli INSERM & Aviesan ITMO BCDE Ambassador, ASAPbio Twitter: #ASAPbio @jessicapolka 1 Publication is essential to scientific progress Adapted from http://asapbio.org/survey Twitter: #ASAPbio @jessicapolka 3 Publishing isn’t what it used to be Ron Vale, bioRxiv/PNAS 2015 Twitter: #ASAPbio @jessicapolka 4 What to do about it? Problem: fast and open venues are not always ‘impactful’ venues Twitter: #ASAPbio @jessicapolka 5 A preprint is a manuscript posted online before journal-organized peer review Twitter: #ASAPbio @jessicapolka 6 Preprints & journals are compatible Berg et al Science7 2016 Preprint servers have existed for 25 years arXiv: 100,000 manuscripts per year In Biology 8 Preprints are taking off inbiology off taking are Preprints Version 1000 100 200 300 400 500 600 700 800 900 0 1 | asapbio.org janv.-03 juil.-03 janv.-04 arXiv (q-bio w/cross-lists, from arxiv.org stats) bioRxiv (from bioRxiv) PeerJ Preprints (bio/med/life) F1000 Research The Winnower Nature Precedings (manuscripts, from search results) Preprints.org (articles/reviews bio/life/med) in figshare by (filtered PrePubMed) juil.-04 janv.-05 juil.-05 janv.-06 juil.-06 janv.-07 juil.-07 janv.-08 juil.-08 janv.-09 juil.-09 janv.-10 juil.-10 janv.-11 juil.-11 janv.-12 juil.-12 janv.-13 juil.-13 janv.-14 juil.-14 janv.-15 juil.-15 janv.-16 juil.-16 9 •Benefits of preprints •Concerns surrounding preprints •Taking action •Recent updates 10 Problem: Lack of access to literature Preprints are immediately available to everyone around -
New Insights Into Oviposition Preference of 5 Trichogramma Species Joël Meunier
New insights into oviposition preference of 5 Trichogramma species Joël Meunier To cite this version: Joël Meunier. New insights into oviposition preference of 5 Trichogramma species. 2021, pp.100008. 10.24072/pci.zool.100008. hal-03325559 HAL Id: hal-03325559 https://hal.archives-ouvertes.fr/hal-03325559 Submitted on 25 Aug 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. New insights into oviposition preference of 5 Trichogramma species Joel Meunier based on reviews by Kévin Tougeron and Eveline C. Verhulst A recommendation of: Up and to the light: intra- and interspecific variability of photo- and geo- tactic oviposition preferences in genus Trichogramma Burte, V., Perez, G., Ayed, F. , Groussier, G., Mailleret, L., van Oudenhove, L. and Calcagno, V.(2021), bioRxiv, 2021.03.30.437671, ver. 4 peer-reviewed and recommended by Peer Community in Zoology Open Access https://doi.org/10.1101/2021.03.30.437671 Submitted: 02 April 2021, Recommended: 17 August 2021 Published: 25 August 2021 Recommendation Copyright: This work is licensed under the Creative Commons Insects exhibit a great diversity of life-history traits that often vary not only Attribution-NoDerivatives 4.0 International License. -
A Community Perspective on the Concept of Marine Holobionts: Current Status, Challenges, and Future Directions
A community perspective on the concept of marine holobionts: current status, challenges, and future directions Simon M. Dittami1, Enrique Arboleda2, Jean-Christophe Auguet3, Arite Bigalke4, Enora Briand5, Paco Cárdenas6, Ulisse Cardini7, Johan Decelle8, Aschwin H. Engelen9, Damien Eveillard10, Claire M.M. Gachon11, Sarah M. Griffiths12, Tilmann Harder13, Ehsan Kayal2, Elena Kazamia14, Francois¸ H. Lallier15, Mónica Medina16, Ezequiel M. Marzinelli17,18,19, Teresa Maria Morganti20, Laura Núñez Pons21, Soizic Prado22, José Pintado23, Mahasweta Saha24,25, Marc-André Selosse26,27, Derek Skillings28, Willem Stock29, Shinichi Sunagawa30, Eve Toulza31, Alexey Vorobev32, Catherine Leblanc1 and Fabrice Not15 1 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France 2 FR2424, Station Biologique de Roscoff, Sorbonne Université, CNRS, Roscoff, France 3 MARBEC, Université de Montpellier, CNRS, IFREMER, IRD, Montpellier, France 4 Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich-Schiller-Universität Jena, Jena, Germany 5 Laboratoire Phycotoxines, Ifremer, Nantes, France 6 Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden 7 Integrative Marine Ecology Dept, Stazione Zoologica Anton Dohrn, Napoli, Italy 8 Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRA, Grenoble, France 9 CCMAR, Universidade do Algarve, Faro, Portugal 10 Laboratoire des Sciences Numériques de Nantes (LS2N), Université -
Passport for Open Science Is a Guide Designed to Accompany You at Every Step Glossary
A PRACTICAL GUIDE FOR PHD STUDENTS Preamble Open science was born out of the new opportunities the digital revolution offered for sharing and disseminating scientific content. It essentially consists of making research results accessible for all by removing any technical or financial barriers which may hinder access to scientific publications. It also involves opening researchers' Index 'black boxes' containing the data and methods used for publications to share these as much as possible. 1. Planning an open approach to scientific work Choosing open science first of all means affirming that research which is mainly financed by public funds must report its results back to the public in as much Using freely accessible resources ................................ p. 6 detail as possible. It is also based on the observation that openness guarantees Planning data management ......................................... p. 8 better documented and more substantiated research and that sharing Working in a reproducible way: strengthens the cumulative nature of science thus encouraging its progress. For yourself, for others ................................................ p. 11 Open transparent science also helps enhance research's credibility in society and the health crisis of 2020 has indeed reminded us how important this issue is. Finally, open science is the bearer of a profound movement towards democratising 2. Disseminating research knowledge to benefit organisations, companies, citizens and particularly students Disseminating your publications in open access ......... p. 16 for whom easy access to knowledge is a condition for success. Making your thesis freely accessible ........................... p. 21 Open science policies now have support at the highest level from the European Making research data open ........................................ p. 25 Union which has made open publication a condition for its support for scientific research since 2012 and by major research organisations around the world such as the National Institutes of Health in the United States. -
On the Efficacy of Restoration in Stream Networks: Comments, Critiques, and Prospective Recommendations
bioRxiv preprint doi: https://doi.org/10.1101/611939; this version posted May 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. RESEARCH ARTICLE On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations Cite as: Murray-Stoker, D. (2020). On the efficacy of restoration in stream 1,2 networks: comments, critiques, and David Murray-Stoker prospective recommendations. bioRxiv, 611939, ver. 7 peer- 1 reviewed and recommended by PCI Odum School of Ecology, University of Georgia, Athens, GA 30602, U.S.A. Ecology. doi: 10.1101/611939 2 Present Address: Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada Posted: 14th April 2020 Recommender: Karl Cottenie This article has been peer-reviewed and recommended by Reviewers: Peer Community in Ecology Eric Harvey and Mariana Perez Rocha (https://doi.org/10.24072/pci.ecology.100052) Correspondence: [email protected] ORCID: https://orcid.org/0000-0002- 4774-6948 PEER COMMUNITY IN ECOLOGY 1 bioRxiv preprint doi: https://doi.org/10.1101/611939; this version posted May 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. ABSTRACT Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. -
Building Synthetic Cellular Organization
M BoC | PERSPECTIVE Building synthetic cellular organization Jessica K. Polka and Pamela A. Silver Department of Systems Biology, Harvard Medical School, Boston, MA 02115; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115 ABSTRACT The elaborate spatial organization of cells enhances, restricts, and regulates pro- Monitoring Editor tein–protein interactions. However, the biological significance of this organization has been Keith G. Kozminski difficult to study without ways of directly perturbing it. We highlight synthetic biology tools University of Virginia for engineering novel cellular organization, describing how they have been, and can be, used Received: Jul 30, 2013 to advance cell biology. Revised: Sep 19, 2013 Accepted: Sep 24, 2013 INTRODUCTION Synthetic biology seeks to use cellular modularity to predictably WHY ORGANIZE? build living systems that do useful things. Historically, many of the Specifying molecular localization provides a powerful way of fruits of the field have been genetic circuits—elements that can re- selecting for and against biological interactions resulting in member, report on stimuli, and perform simple computational tasks. tunable mechanisms for regulation (Figure 1). Thus, confining Other engineered products include synthetic genomes, as well as free diffusion, either by reducing its dimensionality or by corral- proteins endowed by design with novel functions. ling it in a physical compartment, not only can protect proteins Synthetic biology’s engineering principles can also be ap- from off-target effects, but also can enhance desirable interac- plied to interrogate and perturb natural cellular function. In fact, tions. For example, the reduction of diffusion dimensionality can nearly every article published in Molecular Biology of the Cell reduce the search time for finding an on-target interaction.