Researchers Changing the Way We Respond to Epidemics with Wikipedia and Twitter

“A global disease-forecasting system will change the way we respond to epidemics.”  Dr. Sara Del Valle, Los Alamos National Laboratory

The media and broad scientific community have taken note of a fast-growing segment of research known as digital epidemiology. Examples:

  • A system to forecast 28 days in advance where influenza will strike hardest based on localized Wikipedia searches
  • A basis for predicting which communities will see more cases of flu resulting from vaccination decisions as revealed by geographically-based Twitter sentiments.
map

Figure 1. Map generated by more than 250 million public tweets with high-resolution location information, March 2011 – January 2012. Inset shows greater Los Angeles area. Brightness of color corresponds to geographic density of tweets. doi:10.1371/journal.pcbi.1002616.g001

Described by PLOS Computational Biology Associate Editor Marcel Salathé as a “mix of exciting science, modern everyday technology and public health,” this interdisciplinary approach is developing just in time to meet increased demand for improved forecasting of infectious disease outbreaks before they reach epidemic or pandemic stages.

A significant driver for the quantitative and qualitative breakthroughs setting these papers apart from previous work in the field was the openness of the raw data underlying their findings and the source codes underlying their models, as well as the openness of the research processes and final publications.

PLOS journals and blogs actively cover this transformational research:

  • “Digital data sources, when harnessed appropriately, can provide local and timely information about disease and health dynamics in populations around the world,” write PLOS Computational Biology Editors in Editors Outlook: Digital Epidemiology, published 26 Jul 2012
  • “In the same way we check the weather each morning, individuals and public health officials can monitor disease incidence and plan for the future based on today’s forecast,” says Sara Del Valle, coauthor of the PLOS Computational Biology research article, Global Disease Monitoring and Forecasting with Wikipedia, published November 13, 2014

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Publishing Initiatives at PLOS: Improving the Author Experience

The last few months have brought exciting developments at PLOS, and we’ll be doing more in 2015 to make the publishing experience with PLOS even better. Today’s post will talk about just some of what is new now and due in the near term.  We will have much more coming as the year progresses.

We are implementing a number of exciting publishing-related changes aimed at improving the author and community experience. Specifically, these projects aim to reduce time to publication, reduce post-publication correction rates, and above all, provide our community greater access to scientific research – the reason PLOS exists.  Many of these projects will occur behind the scenes and will serve as the pillars of future initiatives, while others will be more visible to the community.

New PDF Design

One of these foundational projects began late last year, aimed at optimizing our production processes for speed and accuracy.  We have implemented a new, single column PDF design that will enable a more efficient composition process, while improving readability on the variety of devices used by the community.  This month, in order to streamline the editorial and production processes across all the journals, we added guidance and information to our author instructions. These new requirements set the foundation for more automated processes that will increase the speed with which PLOS makes published research available online.

New Composition Vendor

In addition we have been shifting workflows and vendors behind the scenes, including transitioning to a new composition vendor. These changes are focused on improving our quality assurance and typesetting processes, and increasing overall publishing efficiency across all seven of our journals.   Results that authors and readers will see in coming weeks and months include continuous publishing schedules for all journals (not just PLOS ONE), whereby papers are published as soon as they are ready; a new tool for authors that will actively assist them in preparing figures for submission; and the gradual introduction of an author proofing step for several journals later this year.

A Temporary Slow-Down for Long Term Gains 

These changes require that PLOS build out new and improved workflows and carefully develop new ways of handling the thousands of manuscripts received each month. In the short term, this will certainly affect our speed to publication and publication volumes. Readers and authors may notice this, but the end result will be gains in speed, efficiency, and quality that will be worth the delays during this transition.

While we work to achieve these ambitious goals, we appreciate the patience shown by our authors and our community.  We’re excited to carry on our mission to accelerate progress in science and medicine by leading a transformation in research communication and thank our many supporters and contributors who make this work possible.

 


 

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Formatting Your Article for Submission: Updated figures, tables, new reference style and LaTex template

PLOS has recently updated our formatting requirements for submitted manuscripts across all seven of our journals. These changes allow us to streamline some of our production work, reducing the overall time to publication for the average article.

As an author, you can help your manuscript move quickly and smoothly through our editorial and production process by properly formatting your submission. Where these guidelines are not followed, the manuscript may be returned to you before we can proceed with an accept decision, and this will slow the time to publication.

Read below about some of the key changes, or use our author guidelines located at the end of this post for a full picture of how to submit and prepare your submission.

Figure Updates

PLOS has updated some of our figure requirements, most notably regarding naming conventions for citations, captions and files themselves. Below is a quick snapshot of these changes, but read our Figure Guidelines for our full requirements:

  • Refer to your figure in-text citations as “Fig. #”, for instance, “Fig. 1” or “Fig. 2”.
  • Ensure that your figure file names also match this formatting, as “Fig#.file extension”. For example, “Fig1.tif” or “Fig2.eps”.
  • Each figure should be single page.
  • Place your figure legends after the paragraph where the figure is first cited.

We are working with one of our vendors on a new tool that will allow authors to easily check their figures for compliance, and in some cases automatically format the figures themselves. The tool is in testing now, and we hope to make it available to authors as soon as possible.

New Reference Style

PLOS has adopted a standard reference style, NLM/ICMJE. Please ensure your reference list is properly formatted to this style guide. You can also download the PLOS reference style at EndNote.

Tables and Boxes

Tables and boxes should now be placed with their legends in the text of the manuscript, after the paragraph where the table is first cited. This will allow for faster processing as well as easier reading for our editors and reviewers. Please be sure your tables are cell-based in Word, or embedded from Excel.

Supporting Information Updates

Supporting Information in-text citations and captions should meet PLOS’ standard style, which is “S# Category”. Common categories include Appendix, Checklist, Dataset, Figure, File, Movie, Protocol, Supporting Information, Table, Text, Video.  For example, “S1 Appendix” or “S2 Table”

The file name should also match the format of the in-text citation and the caption, as “S#_Category.file extension”. For example “S1_Appendix.doc” or “S2_Table.xls”.

New LaTeX Template

In order to provide better services for authors writing in LaTeX, PLOS has revised our LaTeX template to allow for much greater flexibility in handling packages and macros. Please use this template when preparing your LaTeX submission. For further information on LaTeX submissions to PLOS journals, read through our guidelines. Where this template is not used, the manuscript may be returned to you before we can proceed with an accept decision, and this will slow the time to publication.

Our staff will be available to assist you as your manuscript moves through our review process, and if accepted, through our composition process. Thank you for your support of PLOS and open-access.

PLOS ONE Manuscript Guidelines

PLOS Medicine Manuscript Guidelines

PLOS Biology Manuscript Guidelines

PLOS Computational Biology Manuscript Guidelines

PLOS Genetics Manuscript Guidelines

PLOS Pathogens Manuscript Guidelines

PLOS Neglected Tropical Diseases Manuscript Guidelines

 

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PLOS Announces Website Redesign

PLOS is pleased to announce the redesign of PLOS.org, which completes phase two of our website overhaul. The new landing page now enables visitors to navigate more quickly and easily to the information they need. Highlights of the new site also include a rotating carousel of PLOS’ most recent announcements, a news feed and a featured article from our suite of journals.

Phase one of our overhaul  last year included updates to the journal websites. We are always looking to improve. Please send PLOS feedback as you navigate the new site. Comments are welcome at feedback@plos.org. Thank you for supporting PLOS and its mission to transform research communication.

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PLOS Welcomes CC v4.0 Licenses

PLOS has been using the Creative Commons Attribution (CC BY) license for almost 10 years as the default for the research that it publishes. On November 25, 2013, Creative Commons unveiled the next generation of open licenses to support the sharing of content. The new licenses are the result of an open community process with stakeholders from a wide range of domains, including research, education, and the creative arts, and PLOS is proud to have been involved in the effort to make the licenses work for researchers.

Two aspects of the Version 4.0 licenses are particularly important for researchers because they address issues that could have made reuse of published research more cumbersome. Firstly, the re-use rights for data within an article are made clearer and more consistent between different countries and regions.

Second, the licenses provide flexibility on attribution. This is important for research, and particularly for text and data mining, where a multitude of articles might be analyzed together. It doesn’t make sense to list every paper analyzed with each and every search result. It does make sense to link from each result to a page recognizing all the contributions. The new licenses still absolutely require attribution but allow all attributions to a large corpus to be collected together.

Another important aspect of the new licenses is that they combine the experience of several years of developing localized license variants into one international license, ensuring global compatibility and ease of use for all researchers, wherever they may be based.

PLOS will be publishing new articles under CC BY v4.0 beginning in mid-December for PLOS ONE and from January 1, 2014 for all other PLOS journals.

The CC BY license has long been an important part of realizing our aim, of creating the largest possible pool of accessible, re-usable and interoperable research content possible. Open Access is about more than content being free to read; it must also be free to re-use, and re-combine, not just with other articles, but with all forms of research information. The new version of the Creative Commons licenses, the global standard for web based content, is an important part of the toolkit for making that vision possible.

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Letter to the Editor of Science, by Elizabeth Marincola

The following ‘letter to the editor’ was submitted to Science October 4, 2013 and was published on Sciencemag.org December 5, 2013.

_____________________________________________

John Bohannon’s News story “Who’s afraid of peer review?” (special section on Communication in Science, 4 October, p. 60) incriminates many Open Access (OA) journals. Our journal, PLOS ONE, was not implicated. It rejected the fraudulent paper promptly and for the right reasons, as Bohannon acknowledges. Still, the “study” was disappointing: It was not controlled, which would have required seeking to entrap a matched set of closed-access journals, yet it claims that a source of the problem is open access. It then concludes that profitability for OA journals is driven by volume, without acknowledging that the same is true for closed-access journals.  The issues raised by Bohannon’s exercise are not about open access journals; they are about science and technical publishing and the peer review processes used throughout the industry.

In the short term, all scientific publishers have a responsibility to reinforce and strengthen pre-publication review. We must improve the efficiency of peer review and continue to perform checks that uncover conflicts of interest, identify financial disclosures, confirm author affiliations, and ensure compliance with international standards of animal and human testing.

Even with these tools, peer review will never be flawless. As Editor-in-Chief Marcia McNutt points out, it is “time-honored” and “the gold standard” (Editorial, p. 13), but that doesn’t mean our methods of evaluation can’t and shouldn’t be improved. This is the real challenge. And this is why PLOS is working to transform scientific communication by developing better measures of scientific quality both before publication (currently traditional peer review) and after publication (currently the dreaded impact factor).

To this end, PLOS is developing Article Level Metrics (ALMs) that enable the scientific community itself to confer on a research contribution its credibility, relevance, and importance, independent of the journal in which it is published. Peer review at its best is a continual process of critique and assessment.

Elizabeth Marincola

Chief Executive Officer, The Public Library of Science, San Francisco, CA 94111, USA. E-mail: emarincola@plos.org
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Sign up today to have Amazon donate to PLOS

Now when you shop with Amazon, via AmazonSmile, 0.5% of eligible purchases can be donated to PLOS, at no cost to you.

PLOS will direct proceeds from this program to support authors who are unable to pay all or part of their publication fees.

Sign up today to help PLOS remove barriers to participation in Open Access publishing.

Remember: PLOS only benefits when you purchase through smile.amazon.com (not amazon.com). Initially you select “Public Library of Science” as your charitable organization and it should autoload on each visit.

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ANNOUNCING THE RECIPIENTS FOR THE ACCELERATING SCIENCE AWARD PROGRAM

The three award recipients for the Accelerating Science Award Program (ASAP)  were announced today in Washington, DC at the Open Access Week kickoff event hosted by the Scholarly Publishing and Academic Resources Coalition (SPARC) and the World Bank. ASAP recognizes the use of scientific research, published through Open Access, that has led to innovations benefiting society. Major sponsors include the Wellcome Trust, PLOS and Google.

From left: Carlos Rossel of The World Bank, Robert Kiley of Wellcome Trust, Daniel Mietchen, Alex Kozak of Google, Nitika Pant Pai, Elizabeth Marincola of PLOS, Matt Todd, Heather Joseph of SPARC (click photo to view)

 

 

 

 

 

 

The award recipients, along with the challenges they address and their innovative approaches, include:

  • Global Collaboration to Fight Malaria (Matthew Todd, PhD):  At least one child dies of malaria every minute of every day, mainly in Africa and Asia. According to Matthew Todd, who leads the Open Source Malaria Consortium, given minimal financial incentives for pharmaceutical companies to develop new treatments and a high degree of suffering among the affected communities, a large-scale and open collaborative research model provides a solution. Todd turned publicly available data into a global effort to help identify new anti-malaria drugs.  He did this by creating an open source collaboration involving scientists, college students and others from around the world. They use open online laboratory notebooks in which their experimental data is posted each day, enabling instant sharing and the ability to build on others’ findings in almost real time. 

“This recognition may help enlist more people into the collaborative effort to fight malaria,” said Dr. Matthew Todd. “If we succeed with these efforts, the approach could be extended to fighting other diseases – such as cancer.”

 

  • HIV Self-Test App Empowers Patients (Nitika Pant Pai, MD, MPH, PhD, Caroline Vadnais, Roni Deli-Houssein and Sushmita Shivkumar):  To increase awareness, knowledge and access to a convenient HIV screening option, and to expedite connections to treatment in nations hardest hit by the disease, Dr. Nitika Pant Pai and medical staff at McGill University and McGill University Health Centre, Montreal, developed a smartphone application as part of a self-testing strategy that synergized the Internet, an oral fluid–based self-test and a smartphone. This integrated approach included HIV education, an online test to determine HIV risk level, instructions to self-testing and interpreting the results, and confidential linkages and resources for referrals to trained counselors. The personalized smartphone application, developed on the basis of original research published in multiple Open Access journals, helps circumvent the social visibility associated with HIV testing in a healthcare facility. The application could alleviate fears of stigma and discrimination and make HIV detection simple, non-judgmental and confidential while empowering individuals with distilled scientific knowledge.

 

“Being an award recipient will help shine light on the fact that open access acts like a catalyst – by allowing unrestricted knowledge sharing – it exponentiates the power of knowledge to transform and impact lives beyond borders, boundaries, languages, and regions; facilitates creation of novel innovations, improved practices and policies,”  said Dr. Nitika Pant Pai. “With our synergistic innovation (application), we created a patient desired non-judgmental, private option that empowers proactive individuals to self-educate, stage, and seek linkages for HIV.”

 

  • Visualizing Complex Science (Daniel Mietchen, PhD, Raphael Wimmer and Nils Dagsson Moskopp): Many aspects critical to understanding science, experiments and the natural world are hard to convey using only words and diagrams. Good quality multimedia can help make that understanding easier. Daniel Mietchen and his group created the Open Access Media Importer (OAMI), a bot that can find and download supplementary multimedia files from reusably licensed Open Access research articles deposited in PubMed Central and uploads them to Wikimedia Commons, the media  repository used by the Wikipedias and their sister projects.  To date, the bot has uploaded more than 14,000 files that are being used in more than 200 English Wikipedia articles and many more in other languages that together garner about three million monthly views.

 

“We want people to play around with scientific materials and to engage with scientific processes,” said Dr. Daniel Mietchen. “Scientific research should play a more public role in our society, and open licenses greatly facilitate that. We are glad that the award highlights the value of reusing, revising, remixing and redistributing Open Access materials.”

OAs award recipients, these individuals and teams are being honored for addressing a real-world challenge by reusing previously published Open Access research to make a difference in science, medicine, business, technology or society as a whole.  Open Access is the free, immediate online availability of articles, coupled with the rights to use these articles fully as long as the author and the original source are properly attributed.

Photos and video interviews of the winning recipients and honorable mentions can be found at https://sites.google.com/site/asaptoolkit/ .  Additional information on ASAP can be found at http://asap.plos.org/

The ASAP program sponsors share a commitment to affect policy and public understanding to support the adoption of Open Access. They include the Association of College & Research Libraries (ACRL), the Association of Research Libraries (ARL), Co-Action Publishing, Copernicus Publications, Creative Commons, the Directory of Open Access Journals (DOAJ), Doris Duke Charitable Trust, Electronic Information for Libraries (EIFL), eLife, Hindawi, Health Research Alliance (HRA), Howard Hughes Medical Institute, ImpactStory, Jisc, Max Planck Society for the Advancement of Science, Mendeley, Microsoft Research, the Open Access Scholarly Publishers Association (OASPA), Research Councils UK (RCUK), Research Libraries UK (RLUK), Social Science Research Network (SSRN), the Scholarly Publishing and Academic Resources Coalition (SPARC), SURF (Netherlands), the World Bank, and major sponsors Google, PLOS and the Wellcome Trust.

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Professor Grant McFadden Joins PLOS Pathogens as Joint Editor in Chief

PLOS is very pleased to announce that from October 7 2013, Professor Grant McFadden joined Professor Kasturi Haldar as joint Editor in Chief of PLOS Pathogens. Professor McFadden has been associated with PLOS Pathogens from its very beginning in 2005; he became deputy editor in October 2007.

Professor McFadden is based at the University of Florida where his work focuses on how viral pathogens interact with the host immune system.

Dr Virginia Barbour, Medicine Editorial Director for PLOS said “As Deputy Editor, Professor McFadden has been a tremendous advocate for PLOS Pathogens and has been core to developing PLOS Pathogens into the world class journal it is today. We are very pleased to now have him in this position of leadership with Professor Haldar and I Iook forward to working with him and Professor Haldar in the next stage of the journal’s development.”

Professor Haldar said “Grant functioned as a joint Editor in Chief, even as Deputy Editor, so I’m delighted we’ve formalized the situation. The Editorial Board and I would like to thank Grant for all he has done for PLOS Pathogens and look forward to his continuing leadership in the future.”

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Even more journals display ALMs!

In 2009, PLOS became the first (and remains the only) publisher to launch an open source Article-Level Metrics (ALM) app to help other publishers implement ALM on their journals. Now we are pleased to announce that two leading organizations are implementing ALMs using the PLOS open source app.

The Public Knowledge Project (PKP, provides software used by thousands of journals and hosting services to publishers like Co-Action Publishing) and Copernicus Publications (an innovative Open Access publisher) are both launching ALM programs based on the PLOS app.

ALM’s give publishers’ critical insight into the effectiveness of their programs, including highlighting articles that generate the most activity. Other publishers that have introduced ALMs include Biomed Central, eLife, Nature Publishing Group and PeerJ, among others.

Richard Cave, Director of IT for PLOS said “naturally PLOS is particularly gratified when ALMs spread to other journals because of the open source application that we built. PLOS welcomes all publishers who display ALMs because we believe in their power to transform the way research is assessed”.

Juan Pablo Alperin, who lead the development effort for PKP said “like PLOS, we believe that measuring article impact provides a deeper level of understanding about the influence of the work published in journals using our software. We encourage those using OJS systems to sign up for the free ALM service”.

Martin Rasmussen, managing director of Copernicus Publications added “we hope that more publishers will join this initiative and consider implementing it to enable direct comparison across journals”.

PLOS would like to extend a warm ALM welcome to these new journals; we hope these readers enjoy this new dimension to their service.

 

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