22 results on '"Iratxe Puebla"'
Search Results
2. Recommendations for accelerating open preprint peer review to improve the culture of science.
- Author
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Michele Avissar-Whiting, Frédérique Belliard, Stefano M Bertozzi, Amy Brand, Katherine Brown, Géraldine Clément-Stoneham, Stephanie Dawson, Gautam Dey, Daniel Ecer, Scott C Edmunds, Ashley Farley, Tara D Fischer, Maryrose Franko, James S Fraser, Kathryn Funk, Clarisse Ganier, Melissa Harrison, Anna Hatch, Haley Hazlett, Samantha Hindle, Daniel W Hook, Phil Hurst, Sophien Kamoun, Robert Kiley, Michael M Lacy, Marcel LaFlamme, Rebecca Lawrence, Thomas Lemberger, Maria Leptin, Elliott Lumb, Catriona J MacCallum, Christopher Steven Marcum, Gabriele Marinello, Alex Mendonça, Sara Monaco, Kleber Neves, Damian Pattinson, Jessica K Polka, Iratxe Puebla, Martyn Rittman, Stephen J Royle, Daniela Saderi, Richard Sever, Kathleen Shearer, John E Spiro, Bodo Stern, Dario Taraborelli, Ron Vale, Claudia G Vasquez, Ludo Waltman, Fiona M Watt, Zara Y Weinberg, and Mark Williams
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Biology (General) ,QH301-705.5 - Abstract
Peer review is an important part of the scientific process, but traditional peer review at journals is coming under increased scrutiny for its inefficiency and lack of transparency. As preprints become more widely used and accepted, they raise the possibility of rethinking the peer-review process. Preprints are enabling new forms of peer review that have the potential to be more thorough, inclusive, and collegial than traditional journal peer review, and to thus fundamentally shift the culture of peer review toward constructive collaboration. In this Consensus View, we make a call to action to stakeholders in the community to accelerate the growing momentum of preprint sharing and provide recommendations to empower researchers to provide open and constructive peer review for preprints.
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- 2024
- Full Text
- View/download PDF
3. Preprints as a driver of open science: Opportunities for Southeast Asia
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Dasapta Erwin Irawan, Hilyatuz Zahroh, and Iratxe Puebla
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research integrity ,open science ,preprints ,reproducibility ,Southeast Asia ,open access ,Bibliography. Library science. Information resources - Abstract
Southeast Asia is an emerging force of open access scholarly output. For example, Indonesia is in a tight competition with United Kingdom as the largest publisher of open access journals and the second largest producer of open access articles in the world (according to DOAJ and the COKI OA Dashboard, respectively). However, this support for open practices is not yet reflected in institutional research policies in Southeast Asian countries, which still rely on criteria influenced by world university rankings that focus on publication outputs and do not incorporate elements related to research culture, integrity, or open science. Preprints have gained increasing attention across disciplines in the last few years, but they are still not included in institutional policies in SouthEast Asia. This paper discusses the potential for preprints to be a driving force for open science and for quality and integrity in scholarly outputs from Southeast Asia. There is a fledgling preprinting culture in the region, catalyzed by the RINarxiv preprint server in Indonesia and the Malaysia Open Science Platform. We argue that preprints have many advantages: opportunities for open access and for researchers to maintain copyright to their work, wide dissemination, encouraging feedback and critical thinking, and community governance. With these advantages, preprints can become a fast and open communication hub between researchers and all stakeholders in the research process. We recommend regulatory and practical steps to incorporate preprints into science policy and researchers' practices as an effort to promote research integrity, open data and reproducibility.
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- 2022
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4. Recommendations for empowering early career researchers to improve research culture and practice.
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Brianne A Kent, Constance Holman, Emmanuella Amoako, Alberto Antonietti, James M Azam, Hanne Ballhausen, Yaw Bediako, Anat M Belasen, Clarissa F D Carneiro, Yen-Chung Chen, Ewoud B Compeer, Chelsea A C Connor, Sophia Crüwell, Humberto Debat, Emma Dorris, Hedyeh Ebrahimi, Jeffrey C Erlich, Florencia Fernández-Chiappe, Felix Fischer, Małgorzata Anna Gazda, Toivo Glatz, Peter Grabitz, Verena Heise, David G Kent, Hung Lo, Gary McDowell, Devang Mehta, Wolf-Julian Neumann, Kleber Neves, Mark Patterson, Naomi C Penfold, Sophie K Piper, Iratxe Puebla, Peter K Quashie, Carolina Paz Quezada, Julia L Riley, Jessica L Rohmann, Shyam Saladi, Benjamin Schwessinger, Bob Siegerink, Paulina Stehlik, Alexandra Tzilivaki, Kate D L Umbers, Aalok Varma, Kaivalya Walavalkar, Charlotte M de Winde, Cecilia Zaza, and Tracey L Weissgerber
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Biology (General) ,QH301-705.5 - Abstract
Early career researchers (ECRs) are important stakeholders leading efforts to catalyze systemic change in research culture and practice. Here, we summarize the outputs from a virtual unconventional conference (unconference), which brought together 54 invited experts from 20 countries with extensive experience in ECR initiatives designed to improve the culture and practice of science. Together, we drafted 2 sets of recommendations for (1) ECRs directly involved in initiatives or activities to change research culture and practice; and (2) stakeholders who wish to support ECRs in these efforts. Importantly, these points apply to ECRs working to promote change on a systemic level, not only those improving aspects of their own work. In both sets of recommendations, we underline the importance of incentivizing and providing time and resources for systems-level science improvement activities, including ECRs in organizational decision-making processes, and working to dismantle structural barriers to participation for marginalized groups. We further highlight obstacles that ECRs face when working to promote reform, as well as proposed solutions and examples of current best practices. The abstract and recommendations for stakeholders are available in Dutch, German, Greek (abstract only), Italian, Japanese, Polish, Portuguese, Spanish, and Serbian.
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- 2022
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- View/download PDF
5. A guide to preprinting for early-career researchers
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Cassandra L. Ettinger, Madhumala K. Sadanandappa, Kıvanç Görgülü, Karen L. Coghlan, Kenneth K. Hallenbeck, and Iratxe Puebla
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preprints ,early-career researchers ,how-to guide ,open science ,advice ,life sciences ,Science ,Biology (General) ,QH301-705.5 - Abstract
The use of preprints, research manuscripts shared publicly before completing the traditional peer-review process, is becoming a more common practice among life science researchers. Early-career researchers (ECRs) benefit from posting preprints as they are shareable, citable, and prove productivity. However, preprinting a manuscript involves a discussion among all co-authors, and ECRs are often not the decision-makers. Therefore, ECRs may find themselves in situations where they are interested in depositing a preprint but are unsure how to approach their co-authors or advisor about preprinting. Leveraging our own experiences as ECRs, and feedback from the research community, we have constructed a guide for ECRs who are considering preprinting to enable them to take ownership over the process and to raise awareness about preprinting options. We hope that this guide helps ECRs to initiate conversations about preprinting with co-authors and encourage them to preprint their future research.
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- 2022
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- View/download PDF
6. Promoting constructive feedback on preprints with the FAST principles
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Sandra Franco Iborra, Jessica Polka, and Iratxe Puebla
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Point of view ,preprints ,peer review ,peer review of preprints ,FAST principles ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Ensuring that public feedback on preprints is focused, appropriate, specific and transparent (or FAST) will help to develop a thriving culture for reviewing and commenting on preprints.
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- 2022
- Full Text
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7. Responsible handling of ethics in data publication.
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Daniella Lowenberg and Iratxe Puebla
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Biology (General) ,QH301-705.5 - Abstract
A global working group has developed recommendations for the responsible handling of the growing range of ethics cases related to data publication, but further community work is needed toward a responsible and cohesive data publishing ecosystem.
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- 2022
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8. Impact of a short version of the CONSORT checklist for peer reviewers to improve the reporting of randomised controlled trials published in biomedical journals: study protocol for a randomised controlled trial
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Matthias Briel, Sally Hopewell, Iratxe Puebla, and Michael Maia Schlüssel
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Medicine - Published
- 2020
- Full Text
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9. Advancing the culture of peer review with preprints
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Michele Avissar-Whiting, Frederique Belliard, Stefano M Bertozzi, Amy Brand, Katherine Brown, Géraldine Clément-Stoneham, Stephanie Dawson, Gautam Dey, Daniel Ecer, Scott C Edmunds, Tara D. Fischer, Ashley Farley, Maryrose Franko, James Fraser, Kathryn Funk, Clarisse Ganier, Melissa Harrison, Anna Hatch, Haley Hazlett, Samantha Hindle, Daniel W Hook, Phil Hurst, Sophien Kamoun, Robert Kiley, Michael M Lacy, Marcel LaFlamme, Rebecca Lawrence, Thomas Lemberger, Maria Leptin, Elliott Lumb, Catriona MacCallum, Christopher Steven Marcum, Gabriele Marinello, Alex Mendonça, Sara Monaco, Kleber Neves, Damian Pattinson, Jessica Polka, Iratxe Puebla, Martyn Rittman, Stephen J. Royle, Daniela Saderi, Richard Sever, Kathleen Shearer, John Spiro, Bodo Stern, Dario Taraborelli, Ron Vale, Claudia Vasquez, Ludo Waltman, Fiona Watt, Zara Y. Weinberg, and Mark Williams
- Abstract
Preprints enable new forms of peer review that have the potential to be more thorough, inclusive, and collegial. In December 2022, 80 researchers and representatives of funders, institutions, preprint servers, journals, indexers, and review services were invited to gather online and at the Janelia Research Campus for a workshop on Recognizing Preprint Peer Review. Sponsored by HHMI, ASAPbio, and EMBO, this meeting aimed to catalyze community consensus and support for preprint peer review and to create model funder, institutional, and journal policies that recognize both preprints with reviews, and reviews of preprints. Here, we make a call to action to stakeholders in the community to help capture the growing momentum of preprint sharing and empower researchers to provide open and constructive peer review for preprints.
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- 2023
10. A guide to preprinting for early-career researchers
- Author
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Madhumala Sadanandappa, Kıvanç Görgülü, Kenneth Hallenbeck, Karen Coghlan, Cassandra Ettinger, and Iratxe Puebla
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Humans ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology ,Research Personnel - Abstract
The use of preprints, research manuscripts shared publicly before completing the traditional peer-review process, is becoming a more common practice among life science researchers. Early-career researchers (ECRs) benefit from posting preprints as they are shareable, citable, and prove productivity. However, preprinting a manuscript involves a discussion among all co-authors, and ECRs are often not the decision-makers. Therefore, ECRs may find themselves in situations where they are interested in depositing a preprint but are unsure how to approach their co-authors or advisor about preprinting. Leveraging our own experiences as ECRs, and feedback from the research community, we have constructed a guide for ECRs who are considering preprinting to enable them to take ownership over the process and to raise awareness about preprinting options. We hope that this guide helps ECRs to initiate conversations about preprinting with co-authors and encourage them to preprint their future research.
- Published
- 2022
11. Let's make our reviews open, starting now
- Author
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Iratxe Puebla
- Abstract
Researchers spend a lot of time doing peer review, and by a lot we are talking about over 100 million hours per year (estimate for 2020 by Aczel et al.). It is a complex and time consuming process that is often presented as a pillar to science dissemination, ...
- Published
- 2022
12. PReF: describing key Preprint Review Features
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Jessica Polka, Iratxe Puebla, Damian Pattinson, Philip Hurst, Gary S. McDowell, Richard Sever, Thomas Lemberger, Michele Avissar-Whiting, Philip N. Cohen, Tony Ross-Hellauer, Gabriel Stein, Kathleen Shearer, Clare Stone, and Victoria Tianjing Yan
- Abstract
Preprints catalyze rapid and open communication of research. A frequent criticism of preprints, however, is their lack of peer review. In recent years, myriad new initiatives have enabled review of preprinted research to be coordinated, collected, and displayed alongside preprints. This provides evaluation and context for readers, as well as feedback for the authors. The processes behind preprint review are diverse and may differ from journal peer review, which can be a challenge for readers seeking to compare and interpret the reviews. To address this, the ASAPbio organized a working group that set out to define key features of preprint review processes. Here, we describe Preprint Review Features (PReF) as descriptors and provide an implementation guide. PReF captures the key elements of preprint review processes using 8 standard key-value pairs. PReF can serve within the descriptions of individual preprint review processes, and act as search filters on indexing services. Widespread adoption of PReF will promote understanding and categorization of preprint review and improve its discoverability.
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- 2022
13. FAST principles for preprint feedback
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Sandra Franco Iborra, Jessica Polka, Sara Monaco, Sharon Ahmad, Maryrose Franko, Shriyaa Mittal, Samantha Hindle, R. Dyche Mullins, Timothy E.J. Behrens, Gautam Dey, and Iratxe Puebla
- Abstract
There has been strong interest in preprint commenting and review activities in recent years. Public preprint feedback can bring benefits to authors, readers and others in scholarly communication, however, the level of public commenting on preprints is still low. This is likely due to cultural barriers, such as fear by authors that criticisms on their paper will bias readers, editors and evaluators, and concerns by commenters that posting a public critique on a preprint by a more senior colleague may lead to retribution. In order to help address these cultural barriers and foster positive and constructive participation in public preprint feedback, we have developed a set of 14 principles for creating, responding to, and interpreting preprint feedback. The principles are clustered around four broad themes: Focused, Appropriate, Specific, Transparent (FAST). We describe each of the FAST principles and designate which actors (authors, reviewers and the community) each of the principles applies to. We discuss the possible implementation of the FAST principles by different stakeholders in science communication, and explore what opportunities and challenges lie ahead in the path towards a thriving preprint feedback ecosystem.
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- 2022
14. A Guide to Preprinting for Early Career Researchers
- Author
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Cassandra Lane Ettinger, Madhumala K. Sadanandappa, Kivanc Görgülü, Karen Coghlan, Kenneth K. Hallenbeck, and Iratxe Puebla
- Abstract
The use of preprints, research manuscripts shared publicly before the traditional peer-review process, is becoming more common in the life sciences. Early career researchers (ECRs) benefit from posting preprints as they are shareable, citable, and prove productivity. However, the decision to preprint a manuscript involves a discussion among all co-authors, and ECRs are often not the decision-makers. Therefore, ECRs may find themselves in situations where they are interested in posting a preprint but are unsure how to approach their co-authors or advisor about preprinting. Leveraging our own experiences as ECRs, and feedback from the research community, we have constructed a guide for ECRs who are considering preprinting - to enable them to take ownership over the process, and to raise awareness about preprinting options. We hope that this guide helps ECRs to initiate conversations about preprinting with co-authors and encourage them to preprint their future research.
- Published
- 2022
15. Preprints: Their Evolving Role in Science Communication
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Iratxe Puebla, Jessica Polka, and Oya Rieger
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- 2022
16. The many shapes of peer review: how to make journal review and preprint review activities more complementary?
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Iratxe Puebla, Jane Alfred, Frederique Belliard, Katherine Brown, Phil Hurst, Nicola Nugent, and Chris Graf
- Abstract
While peer review plays a central role in the evaluation and publication of research findings, there are a number of known challenges related to inefficiencies and lack of diversity in the peer review process at system level. Preprint review activities have received increasing attention in recent years and may provide avenues for addressing some of the current challenges in journal peer review. At a workshop during the Researcher to Reader conference in February 2021, we explored how preprint review activities could be made more complementary with journal review and leveraged to increase diversity in peer review. We summarize the discussions at the workshop covering the benefits and challenges of preprint review for different stakeholders, what a journal-compatible preprint review looks like, and the barriers and potential solutions to make preprint review more complementary with journal review.
- Published
- 2021
17. Empowering Early Career Researchers to Improve Science
- Author
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Brianne A Kent, Constance Holman, Emmanuella Amoako, Alberto Antonietti, JAMES MBA Azam, Hanne Ballhausen, Yaw Bediako, Anat Belasen, Clarissa França Dias Carneiro, Yen-Chung Chen, Ewoud Compeer, Chelsea Connor, Sophia Crüwell, Humberto Debat, Emma Dorris, Hedyeh Ebrahimi, Jeffrey C Erlich, Florencia Fernández Chiappe, Felix Fischer, Małgorzata Anna Gazda, Toivo Glatz, Peter Grabitz, Verena Heise, David Kent, Hung Lo, Gary Mcdowell, Devang Mehta, Wolf-Julian Neumann, Kleber Neves, Mark Patterson, Naomi Penfold, Sophie K. Piper, Iratxe Puebla, Peter Quashie, Carolina Paz Quezada, Julia Lindsay Riley, Jessica L. Rohmann, Shyam Saladi, Benjamin Schwessinger, Bob Siegerink, Paulina Stehlik, Alexandra Tzilivaki, Kate Umbers, Aalok Varma, Kaivalya Walavalkar, Charlotte M de Winde, Cecilia Zaza, and Tracey Lynn Weissgerber
- Abstract
Early career researchers (ECRs) are important stakeholders leading efforts to catalyze systemic change in the conduct and communication of science. Here, we summarize the outputs from a virtual unconventional conference (unconference), which brought together 54 invited experts from 20 countries with extensive experience in ECR initiatives designed to improve science. The event was focused on why ECRs are needed to improve science and the obstacles they face when trying to promote reform. Our discussions also highlighted the additional obstacles that ECRs in countries with limited research funding experience when working to improve the scientific system. We provide the lessons learned from successful ECR-led or ECR-focused initiatives and outline actions that individuals and organizations can take to further support ECRs who are working to improve research culture and practice.
- Published
- 2021
18. From amazing work to I beg to differ - analysis of bioRxiv preprints that received one public comment till September 2019
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Iratxe Puebla
- Published
- 2021
19. Preprints: a tool and a vehicle towards greater reproducibility in the life sciences
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Iratxe Puebla
- Subjects
Open science ,Computer science ,Preprints ,Publication bias ,Publication process ,Data science ,Reproducibility ,PATH (variable) - Abstract
We have seen a number of initiatives arise in recent years aiming to tackle concerns around the reproducibility of published findings. Researchers in the life sciences now have a number of tools at their disposal to boost the reproducibility of their science and preprints have emerged as an instrumental element within this toolkit. Preprints broaden the when, by whom and how of the review and feedback on research compared to the journal publication process, help address publication bias, and can play an important role as a vehicle towards open science practices. Preprints hold further untapped potential to close the gap between discovery and dissemination, and to accelerate the path to a more reproducible research ecosystem.
- Published
- 2020
20. Building trust in preprints: recommendations for servers and other stakeholders
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Jeffrey Beck, Christine A Ferguson, Kathryn Funk, Brooks Hanson, Melissa Harrison, Michele Ide-Smith, Rachael Lammey, Maria Levchenko, Alex Mendonça, Michael Parkin, Naomi Penfold, Nicole Pfeiffer, Jessica Polka, Iratxe Puebla, Oya Y Rieger, Martyn Rittman, Richard Sever, and Sowmya Swaminathan
- Abstract
On January 20 and 21, 2020, ASAPbio, in collaboration with EMBL-EBI and Ithaka S+R, convened over 30 representatives from academia, preprint servers, publishers, funders, and standards, indexing and metadata infrastructure organisations at EMBL-EBI (Hinxton, UK) to develop a series of recommendations for best practices for posting and linking of preprints in the life sciences and ideally the broader research community. We hope that these recommendations offer guidance for new preprint platforms and projects looking to enact best practices and ultimately serve to improve the experience of using preprints for all.
- Published
- 2020
21. Unlock ways to share data on peer review
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Pierpaolo Dondio, Hollydawn Murray, Kalpana Shankar, Phil Hurst, Harry J. J. Blom, Peter W. Rodgers, Duncan Nicholas, Marco Seeber, Joris van Rossum, Giangiacomo Bravo, Flaminio Squazzoni, Bahar Mehmani, Giorgio Pedrazzi, Stephen J. Cowley, Iratxe Puebla, F. Bianchi, Tiago Barros, Ana Marušić, Michael Willis, Catriona J. MacCallum, Virginia Dignum, Petra Ahrweiler, Rachael Lammey, Francisco Grimaldo, Aliaksandr Birukou, Lynsey Haire, Jason Hoyt, and Tony Ross-Hellauer
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0303 health sciences ,Multidisciplinary ,business.industry ,05 social sciences ,data mining ,Public relations ,050905 science studies ,Research management ,Bibliometrics ,Scientometrics ,Research Integrity ,03 medical and health sciences ,Work (electrical) ,Publishing ,Sociology ,0509 other social sciences ,business ,030304 developmental biology - Abstract
Peer review is the defining feature of scholarly communication. In a 2018 survey of more than 11, 000 researchers, 98% said that they considered peer review important or extremely important for ensuring the quality and integrity of scholarly communication.
- Published
- 2020
22. A recombinant H1 histone-based system for efficient delivery of nucleic acids
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Anthony E. Brown, Alison Mortlock, Andrea Crisanti, Iratxe Puebla, Walter Low, and Selma Esseghir
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Genetic Vectors ,Bioengineering ,Gene delivery ,Transfection ,Applied Microbiology and Biotechnology ,law.invention ,Histones ,Histone H1 ,law ,RNA interference ,Cricetinae ,Anopheles ,Chlorocebus aethiops ,Tumor Cells, Cultured ,Animals ,Humans ,RNA, Small Interfering ,Luciferases ,Vero Cells ,Reporter gene ,biology ,DNA ,General Medicine ,Molecular biology ,Recombinant Proteins ,Rats ,Cell biology ,Histone ,COS Cells ,Recombinant DNA ,biology.protein ,Nucleic acid ,RNA Interference ,K562 Cells ,HeLa Cells ,Biotechnology - Abstract
We describe here a unique transfer system based on a truncated form of the human linker histone H1F4 for the delivery of nucleic acids to a variety of cells. The efficiency of truncated histone H1.4F was assessed using both primary mammalian and immortalised insect and mammalian cell lines. Our results indicated that recombinant histone H1.4F was able to deliver DNA, dsRNA and siRNA in all cells tested. Quantitative analysis based on reporter gene expression or silencing of target genes revealed that the transfection efficiency of histone H1.4F was comparable to, or better than, liposome-based systems. Notably, the efficiency of histone H1.4F was associated with very low toxicity for transfected cells. The human H1.4F recombinant protein is easily purified in large-scale from bacterial lysates using inexpensive simplified processing. This versatile transfection system represents an important advance in the field of gene delivery and an improvement over earlier nucleic acid delivery methods.
- Published
- 2003
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