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Progress Update July 2011
PUBLIC LIBRARY of SCIENCE PUBLIC LIBRARY of SCIENCE www.plos.org 3URJUHVV8SGDWH 2010 Progress Update July 2011 www.plos.org Welcome to the 2010 PLoS Progress Update, aimed at keeping our authors, reviewers, editors, and supporters fully apprised of developments at PLoS over our most recent Highlights year. You can sign up to read future updates here. If you would like 1. Message from a fuller historical picture of how far we’ve come, you can read the the Founders 2009 Progress Update and the first full Progress Report. 2. Publishing Initiatives 3. Influential 1. Message from the Founders Research 4. A Growing It’s been another exciting year for PLoS, focused on establishing more open, Organization efficient, and effective ways to accelerate progress in science and medicine 5. The Evolving and leading a transformation in research communication. Open Access Landscape PLoS reached a truly significant milestone in 2010 when, seven years 6. The First PLoS after entering the publishing business, our annual operating revenues Forum exceeded expenses for the first time. Although we are delighted that PLoS and others have now shown that Open Access (OA) is a viable and 7. Customer Service sustainable business model, we have a long way to go before universal 8. Financial Summary access is achieved for all. 9. 2011 and Beyond The significant progress that we’ve made toward this goal could not have 10. Major Support been achieved without the leadership of our co-founder Harold Varmus, in 2010 who announced during the year that he was stepping aside as Chairman 11.
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Scientific Production in the PLOS Journals Sibele Fausto*, Rogério Mugnaini**
Beyond traditional metrics at the University of São Paulo: scientific production in the PLOS journals Sibele Fausto*, Rogério Mugnaini** *[email protected], **[email protected] Escola de Comunicações e Artes, University of São Paulo, Av. Prof. Lúcio M. Rodrigues, 443, São Paulo, SP, CEP 05608-020 (Brazil) INTRODUCTION In the evolution of the Open Access Movement, there have been pioneering initiatives to provide free and open access to published scientific content, such as the creation of the BioMed Central (BMC) and the Public Library of Science (PLOS) in early 2000. These set out a new funding model for journals where the liability for publishing costs is transferred from the readers to the authors. The PLOS was also innovative since it led to the creation of Article-Level Metrics - ALM (Fenner & Lin, 2013) and expanded by issuing a series of new titles - PLOS Biology in 2003; PLOS Medicine in 2004, PLOS Computational Biology, PLOS Genetics and PLOS Pathogens in 2005, PLOS ONE in 2006 and more recently PLOS Currents. As a result, today the set of PLOS journals is widely recognized and prestigious. Recently (on June 18, 2013), PLOS introduced a new search engine - PLOS-ALM Reports (http://almreports.plos.org/) (Allen, 2013) which allows more detailed investigations to be carried out in all the PLOS journals showing consolidated alternative measures of visibility and impact earned by published articles. Since the University of São Paulo is considered to be "Brazil's leading academic institution in research and graduate education" (Schwartzman, 2006), this study is an attempt to find evidence of the USP performance that goes beyond traditional metrics, by using the alternative indicators provided by PLOS-ALM and making a comparison with other articles in the PLOS journals that come from Brazil.
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Regional Reinfection by Dengue: a Network Approach Using Data from Mexico
bioRxiv preprint doi: https://doi.org/10.1101/475137; this version posted November 23, 2018. 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. Regional reinfection by Dengue: a network approach using data from Mexico Mayra Nú~nez-Lópeza;∗, Luis Alarcón-Ramosb, and Jorge X. Velasco-Hernándezc aDepartamento de Matemáticas Aplicadas, ITAM R´ıoHondo 1, CDMX 01080, México bDepartamento de Matemáticas Aplicadas y Sistemas, UAM-Cuajimalpa, Av.Vasco de Quiroga 4871, CDMX 05300, México and cInstituto de Matemáticas, UNAM-Juriquilla, Boulevard Juriquilla No. 3001, Querétaro, 76230, México Most of the recent epidemic outbreaks in the world have a strong immigration component as a trigger rather than the dynamics implied by the basic reproduction number. In this work we present and discuss an approach to the problem of pathogen reinfections in a given area that associates people mobility and transmission of dengue, using a Markov-chain Susceptible-Infected-Susceptible (SIS) metapopulation model over a network. Our model postulates a parameter that we have named the effective inoculum size which represents a local measure of the population size of infected hosts that arrive at a given location as a function of population size, current incidence at neighboring locations and the connectivity of the patches. This parameter can be interpreted as an indicator of outbreak risk of any location.
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Core Standardized Methods for Rapid Biological Field Assessment
CORE STANDARDIZED METHODS FOR RAPID BIOLOGICAL FIELD AssESSMENT EDITED BY TROND H. LARSEN CORE STANDARDIZED METHODS FOR RAPID BIOLOGICAL FIELD AssESSMENT Edited by: Trond H. Larsen Any opinions expressed in this book are those of the writers and do not necessarily reflect Published by: those of Conservation International or its Conservation International co-publishers. 2011 Crystal Drive, Suite 500 Arlington, VA 22202 USA Suggested citation: Tel : +1 703-341-2400 Larsen, T.H. (ed.). 2016. Core Standardized www.conservation.org Methods for Rapid Biological Field Assessment. Conservation International, Cover photos left to right: Arlington, VA. © Trond H. Larsen, © Phil DeVries, © Trond H. Larsen, © Trond H. Larsen, Acknowledgments: © Trond H. Larsen, © Trond H. Larsen, Conservation International thanks the large © Conservation International/Photo by number of authors and their supporting Russell A. Mittermeier, © Trond H. Larsen, institutions for working so diligently and © Trond H. Larsen, © Trond H. Larsen, cooperatively towards the common goal of © Trond H. Larsen this handbook. We are also indebted to the many peer reviewers who helped to improve Back cover photo: this handbook and the protocols therein. This © Trond H. Larsen publication would not have been possible without the coordination and support provided Conservation International is a private, by Travis Thyberg. non-profit organization exempt from federal income tax under section 501c(3) of the Conservation International expresses their Internal Revenue Code. sincere gratitude
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Plos Progress Update 2014/2015 from the Chairman and Ceo
PLOS PROGRESS UPDATE 2014/2015 FROM THE CHAIRMAN AND CEO PLOS is dedicated to the transformation of research communication through collaboration, transparency, speed and access. Since its founding, PLOS has demonstrated the viability of high quality, Open Access publishing; launched the ground- breaking PLOS ONE, a home for all sound science selected for its rigor, not its “significance”; developed the first Article- Level Metrics (ALMs) to demonstrate the value of research beyond the perceived status of a journal title; and extended the impact of research after its publication with the PLOS data policy, ALMs and liberal Open Access licensing. But challenges remain. Scientific communication is far from its ideal state. There is still inconsistent access, and research is oered at a snapshot in time, instead of as an evolving contribution whose reliability and significance are continually evaluated through its lifetime. The current state demands that PLOS continue to establish new standards and expectations for scholarly communication. These include a faster and more ecient publication experience, more transparent peer review, assessment though the lifetime of a work, better recognition of the range of contributions made by collaborators and placing researchers and their communities back at the center of scientific communication. To these ends, PLOS is developing ApertaTM, a system that will facilitate and advance the submission and peer review process for authors, editors and reviewers. PLOS is also creating richer and more inclusive forums, such as PLOS Paleontology and PLOS Ecology Communities and the PLOS Science Wednesday redditscience Ask Me Anything. Progress is being made on early posting of manuscripts at PLOS.
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A Reply to Agrawal
TRPLSC-1176; No. of Pages 1 Letter Open access is worth considering: a reply to Agrawal 1 2 Robert Lanfear and Matthew W. Pennell 1 Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT 2602, Australia 2 Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA In a recent letter to Trends in Plant Science, Anurag A. impact’’. Unfortunately this is a common misconception, Agrawal [1] outlines his opinions on open access (OA) and we would like to set the record straight: many OA publishing. In it, he incorrectly conflates OA journals with journals are highly selective and high impact. nonselective journals. Specifically, Agrawal [1] states that We compiled data on the publication policies and impact ‘a publication in an open access journal only imparts [the factors of 31 popular and reputable OA journals in biology information that it is] ‘‘not scientifically flawed’’’, and later (summarized in Table 1, full version with complete publi- that OA journals provide ‘‘no stamp of rigor or potential cation policy text available at [2]). This list is far from exhaustive; it includes neither all of the popular and Table 1. Publication polices of 31 open-access publishers in reputable OA journals, nor any of the many unpopular a the biological sciences and/or irreputable ones (http://scholarlyoa.com/2014/01/ Journal Selection for novelty Impact b 02/list-of-predatory-publishers-2014/). Rather, the list and/or impact factor comprises a small selection of journals that serves to PLOS Medicine Yes 15.25 demonstrate that many OA journals are both selective PLOS Biology Yes 12.69 and high impact.
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Estimating Drivers of Autochthonous Transmission of Chikungunya Virus in Its Invasion of the Americas – PLOS Currents Outbreaks
10/15/2018 Estimating Drivers of Autochthonous Transmission of Chikungunya Virus in its Invasion of the Americas – PLOS Currents Outbreaks Estimating Drivers of Autochthonous Transmission of Chikungunya Virus in its Invasion of the Americas February 10, 2015 · Research Article Citation Perkins TA, Metcalf CJE, Grenfell BT, Tatem AJ. Estimating Drivers of Autochthonous Transmission of Tweet Chikungunya Virus in its Invasion of the Americas. PLOS Currents Outbreaks. 2015 Feb 10 . Edition 1. doi: 10.1371/currents.outbreaks.a4c7b6ac10e0420b1788c9767946d1fc. Authors T. Alex Perkins Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA; Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA. C. Jessica E. Metcalf Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA. Bryan T. Grenfell Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA; Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA. Andrew J. Tatem Department of Geography and Environment, University of Southampton, Southampton, UK; Flowminder Foundation, Stockholm, Sweden. Abstract Background Chikungunya is an emerging arbovirus that has caused explosive outbreaks in Africa and Asia for decades and invaded the Americas just over a year ago. During this ongoing invasion, it has spread to 45 countries where it has been transmitted autochthonously, infecting nearly 1.3 million people in total. Methods Here, we made use of weekly, country-level case reports to infer relationships between transmission and two putative climatic drivers: temperature and precipitation averaged across each country on a monthly basis. To do so, we used a TSIR model that enabled us to infer a parametric relationship between climatic drivers and transmission potential, and we applied a new method for incorporating a probabilistic description of the serial interval distribution into the TSIR framework.
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PLOS Computational Biology Associate Editor Handbook Second Edition Version 2.6
PLOS Computational Biology Associate Editor Handbook Second Edition Version 2.6 Welcome and thank you for your support of PLOS Computational Biology and the Open Access movement. PLOS Computational Biology is one of the four community run, Open Access journals published by the Public Library of Science. The journal features works of exceptional significance that further our understanding of living systems at all scales—from molecules and cells, to patient populations and ecosystems—through the application of computational methods. Readers include life and computational scientists, who can take the important findings presented here to the next level of discovery. Since its launch in 2005, PLOS Computational Biology has grown not only in the number of papers published, but also in recognition as a quality publication and community resource. We have every reason to expect that this trend will continue and our team of Associate Editors play an invaluable role in this process. Associate Editors oversee the peer review process for the journal, including evaluating submissions, selecting reviewers, assessing reviewer comments, and making editorial decisions. Together with fellow Editorial Board members and the PLOS CB Team, Associate Editors uphold journal policies and ethical standards and work to promote the PLOS mission to provide free public access to scientific research. PLOS Computational Biology is one of a suite of influential journals published by PLOS. Information about the other journals, the PLOS business model, PLOS innovations in scientific publishing, and Open Access copyright and licensure can be found in Appendix IX. Table of Contents PLOS Computational Biology Editorial Board Membership ................................................................................... 2 Manuscript Evaluation .....................................................................................................................................
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Below the Mesophotic C
www.nature.com/scientificreports OPEN Below the Mesophotic C. C. Baldwin1, L. Tornabene2 & D. R. Robertson3 Mesophotic coral ecosystems, which occur at depths of ~40 to 150 m, have received recent scientifc attention as potential refugia for organisms inhabiting deteriorating shallow reefs. These ecosystems merit research in their own right, as they harbor both depth-generalist species and a distinctive reef-fsh Received: 31 August 2017 fauna. Reef ecosystems just below the mesophotic are globally underexplored, and the scant recent literature that mentions them often suggests that mesophotic ecosystems transition directly into Accepted: 12 February 2018 those of the deep sea. Through submersible-based surveys in the Caribbean Sea, we amassed the most Published: xx xx xxxx extensive database to date on reef-fsh diversity between ~40 and 309 m at any single tropical location. Our data reveal a unique reef-fsh assemblage living between ~130 and 309 m that, while taxonomically distinct from shallower faunas, shares strong evolutionary afnities with them. Lacking an existing name for this reef-faunal zone immediately below the mesophotic but above the deep aphotic, we propose “rariphotic.” Together with the “altiphotic,” proposed here for the shallowest reef-faunal zone, and the mesophotic, the rariphotic is part of a depth continuum of discrete faunal zones of tropical reef fshes, and perhaps of reef ecosystems in general, all of which warrant further study in light of global declines of shallow reefs. Studies of deep tropical-reef ecosystems have surged during the past decade1–10. This is due in part to the global decline of shallow coral reefs having sparked interest in the potential for deep reefs to act as refugia for shallow-water organisms stressed by warming surface waters or deteriorating reefs.
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How Faculty Share Research Data?
How Faculty Share Research Data? Yingting Zhang, MLS, AHIP Research Service Librarian RWJ Library of the Health Sciences Rutgers University 2018 VALE Users’/NJLA CUS/NJ ACRL Conference January 5, 2018 RUL Wikipedia Project via Cultural Competence in Health Care Outline • Background / Objectives • Methods • Results • Conclusion 2 RUL Wikipedia Project via Cultural Competence in Health Care Background Data Sharing BioMed Central Open Data Policy https://www.biomedcentral.com/about/policies/open-data 3 RUL Wikipedia Project via Cultural Competence in Health Care Objectives Explore how researchers share their data Understand researchers’ needs better Provide better research support services 4 RUL Wikipedia Project via Cultural Competence in Health Care Methods • PubMed Search • 3/3/2014-6/30/2017 • Results in EndNote • Data Collection • Data Analysis 5 RUL Wikipedia Project via Cultural Competence in Health Care PLOS Journals Searched PLOS ONE PLOS pathogens PLOS genetics PLOS currents PLOS medicine PLOS computational biology PLOS biology PLOS neglected tropical diseases 6 RUL Wikipedia Project via Cultural Competence in Health Care PLOS Acceptable Data-Sharing Methods Data deposition (strongly recommended) Data in supporting information files Data made available to all interested researchers upon request Data available from a third party 7 RUL Wikipedia Project via Cultural Competence in Health Care Results 148 articles (n=148) retrieved from PubMed meeting the search criteria with 84% of them (n=124) published in PLOS One 59% (n=88) of the articles with a statement that the all relevant data are within the paper and / or its Supporting Information files 11% (n=17) papers indicating that data were deposited in a repository with 11 in a subject repository and 6 in a general repository 3 articles stating that data were available upon request and 4 stating that data were available via the third party 36 articles with no Data Availability Statements due to submission before the PLOS Data Policy began to be enforced on March 4, 2013.
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The Digital Scholar
The Digital Scholar How Technology Is Transforming Scholarly Practice Martin Weller BLOOMSBURY ACADEMIC First published in 2011 by Bloomsbury Academic an imprint of Bloomsbury Publishing Plc 36 Soho Square, LondonWiD3QY, UK and 175 Fifth Avenue, NewYork, NY 10010, USA Copyright © Martin Weller 2011 This work is published subject to a Creative Commons Attribution Non-Commercial Licence. You may share this work for non-commercial purposes only, provided you give attribution to the copyright holder and the publisher. For permission to publish commercial versions please contact Bloomsbury Academic CIP records for this book are available from the British Library and the Library of Congress ISBN 978-1-84966-497-4 (hardback) ISBN 978-1-84966-617-6 (paperback) ISBN 978-1-84966-625-1 (ebook) Visit http://bloomsburyacademic.com/ to find out more about our authors and their books. You will find extracts, author interviews, author events and you can sign up for newsletters to be the first to hear about our latest releases and special offers. Coverimage: © PeterPhoto123/Shutterstock To Ellen While industries such as music, newspapers, film and publishing have seen radical changes in their business models and practices as a direct result of new technologies, higher education has so far resisted the wholesale changes we have seen elsewhere. However, a gradual and fundamental shift in the practice of academics is taking place. Every aspect of scholarly practice is seeing changes effected by the adoption and possibilities of new technologies. This book will explore these changes, their implications for higher education, the possibilities for new forms of scholarly practice and what lessons can be drawn from other sectors.
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SCOR Proceedings Volume 54 Plymouth, UK September 2018
SCOR Proceedings 39th SCOR EXECUTIVE COMMITTEE MEETINGVolume 54 Beijing, China 20-22 October 2009 Plymouth, UK September 2018 EXECUTIVE COMMITTEE SCIENTIFIC COMMITTEE ON OCEANIC RESEARCH September 2018 – September 2020 President: Dr. Marie-Alexandrine Sicre Ex-Officio Members: CNRS, LOCEAN Dr. Patricia Miloslavich (IABO) Tour 46-00, 5eme étage GOOS BioEco Project Officer 4 place Jussieu University of Tasmania 75252 Paris Cedex 05 Institute for Marine and Antarctic Studies FRANCE Private Bag 129 E-mail: [email protected] 7001 Hobart TAS AUSTRALIA Secretary: Email: [email protected] Prof. Paul G. Myers Department of Earth and Atmospheric Sciences Prof. Trevor McDougall (IAPSO) 1-26 ESB, University of Alberta The School of Mathematics and Statistics Edmonton, Alberta T6G 2E3 University of New South Wales CANADA Sydney NSW 2052 [email protected] AUSTRALIA Past President: Prof. Joyce Penner (IAMAS) Prof. Peter Burkill Climate and Space Sciences and Engineering Mount Clogg Farm Climate & Space Research Building Shaugh Prior University of Michigan Plymouth PL7 5HA 2455 Hayward Street UNITED KINGDOM Ann Arbor, MI 48109-2143 E-mail: [email protected] USA Vice-Presidents: Co-opted Members: Dr. David Halpern Nuria Casacuberta Arola 14030 Crest Way ETH Zurich Del Mar, CA 92014 Otto-Stern-Weg, 5 USA HPK G23 [email protected] Zurich 8093 SWITZERLAND Dr. Sinjae Yoo [email protected] 2670, Iljudongro Gujwa-eup, Jeju 63349 SCOR Secretariat: SOUTH KOREA Edward R. Urban, Jr., Executive Director Email: [email protected]
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