A Perfect Match: A Multidisciplinary Conference for the Ultimate Multidisciplinary Journal

Despite the ongoing situation in Boston, at this point the Experimental Biology 2013 conference is scheduled to begin this Sunday, and PLOS ONE is looking forward to being there to meet our authors, editors, reviewers, and anyone interested in joining the PLOS ONE community.

We’ll be at booth #547 in the Exhibitor’s Hall, Sunday through Tuesday, 9 am to 4 pm. We will also be hosting an informal meeting at the booth for editors and those interested in joining our editorial board on Monday, April 22, from 12 to 1:30. We hope to see you there!

The conference is an exciting multidisciplinary event, with a variety of participating societies that cover a wide range of biological topics, including the American Society for Biochemistry and Molecular Biology (ASBMB), American Society for Pharmacology and Experimental Therapeutics (ASPET), and the American Physiological Society (APS).

The diversity and breadth of the topics covered at the conference is a perfect match for PLOS ONE. As a multidisciplinary journal, we publish work in all the represented fields, and we are also a great venue for the interdisciplinary work this conference aims to promote. While discipline-specific journals can create artificial barriers between “traditional” research areas, PLOS ONE’s coverage of all fields of science and medicine fosters interdisciplinary research and productive collaboration between fields that might have previously been separated.

We hope to see you at booth #547. For the latest updates on the conference, please visit the conference homepage and follow @ExpBio and #EB2013 on Twitter.

Official launch of journal Pharmacology Research & Perspectives at ASPET-BPS joint meeting

PRP2 short

Boston, MA — April 20, 2013—The American Society for Pharmacology and Experimental Therapeutics (ASPET), British Pharmacological Society (BPS) and John Wiley & Sons have issued a call for papers for their new open access, peer-reviewed journal, Pharmacology Research & Perspectives. The announcement was made as the three partners prepare for the official launch of the journal at the Joint ASPET-BPS Annual Meeting, taking place beginning April 20 as part of the Experimental Biology 2013 conference.

Pharmacology Research & Perspectives (PR&P) will publish original research, reviews and perspectives in all areas of preclinical and clinical pharmacology, therapeutics, education and related research areas. The journal will serve as the first fully open access journal for ASPET and BPS, and joins their combined portfolio of prestigious peer-reviewed subscription-based scientific journals, including Drug Metabolism and Disposition, Journal of Pharmacology and Experimental Therapeutics, Molecular Pharmacology, British Journal of Pharmacology, and British Journal of Clinical Pharmacology.

 Editor-in-Chief Dr Michael J. Curtis commented, “I’m pleased to announce that Pharmacology Research & Perspectives is now open for submissions. ASPET, BPS and Wiley publish high-quality peer-reviewed journals – and our collaboration will continue this tradition.”

Dr Curtis obtained his PhD from the University of British Columbia and has been a Reader at King’s College London since 1996. Dr Curtis has extensive editorial experience, serving as Editor-in-Chief of the Journal of Pharmacological and Toxicological Methods and Reviews Editor of British Journal of Pharmacology, among other positions.

Dr Darrell Abernethy will join the new journal as Deputy Editor. Dr Abernethy’s faculty appointment is with the Johns Hopkins University School of Medicine. He received his MD (AOA) and PhD (Pharmacology) degrees from the University of Kansas School of Medicine. Dr Abernethy is an experienced editor, having served as Editor-in-Chief of Pharmacological Reviews and an Associate Editor of the Journal of Pharmacology and Experimental Therapeutics among other positions.

All articles in PR&P will be published as fully open access under a Creative Commons License on Wiley Online Library and deposited in PubMed Central immediately upon publication. A publication fee will be payable by authors on acceptance of their articles. Authors affiliated with, or funded by, an organization that has a Wiley Open Access Account can publish without directly paying any publication charges.

 The journal expects to publish its first issue in autumn 2013.

Issue 2:2 of Cancer Medicine now live!

Cancer Medicine

You can read Issue 2:2 of Cancer Medicine online now!

The journal brings together articles on a range of oncology specialties, covering cancer biology, clinical cancer research and cancer prevention, with authors from across the globe.

Below are some top articles which Editor-in-Chief Prof. Qingyi Wei has highlighted from the issue.  We hope that you enjoy this exciting new content.

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GM-CSF enhances tumor invasion by elevated MMP-2, -9, and -26 expression
Claudia M. Gutschalk, Archana K. Yanamandra, Nina Linde, Alice Meides, Sofia Depner and Margareta M. Mueller

Summary: In this study we analyze the contribution of granulocyte–macrophage colony-stimulating factor (GM-CSF) to tumor invasion and proteinase expression and activation in HT-29 colon adenocarcinoma cells. We could demonstrate that GM-CSF contributes to tumor progression, enhancing the migratory capacity in vitro and tumor cell invasion into the surrounding tissue and stromal activation such as angiogenesis in vivo. Moreover, in a complex 3D in vitro model, GM-CSF overexpression or treatment was associated with a discontinued basement membrane deposition that might be mediated by the observed increased expression and activation of MMP-2, -9, and -26.

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Complexity in cancer biology: is systems biology the answer?
Evangelia Koutsogiannouli, Athanasios G. Papavassiliou and Nikolaos A. Papanikolaou

Summary: Tumor tissues consist of different types of cells with altered genetic, epigenetic, and protein networks. We propose a simple conceptual model to account for oncogenic and tumor suppressor proteins forming different complexes within and between tumor cells.

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Is there a role for immune checkpoint blockade with ipilimumab in prostate cancer?
Edward Cha and Eric J. Small

Summary: Ipilimumab, a cytotoxic T-lymphocyte antigen 4 (CTLA-4)-blocking monoclonal antibody, is thought to augment natural immune responses to tumors. Ipilimumab is approved in several countries to treat advanced melanoma, and it is now under phase 3 investigation in prostate cancer based on the results of 7 smaller clinical trials, as reviewed in this article.

Cancer Medicine is a peer reviewed, interdisciplinary journal providing rapid publication of cutting-edge research from global biomedical researchers across the cancer sciences.

Submit your paper here>    Sign up for eToC Alerts here>

Paid Gold OA Versus Free Gold OA: Against Color Cacophony

1. The Green/Gold Open Access (OA) distinction concerns whether it is the author or the publisher that provides the OA.

2. This distinction was important to mark with clear terms because the conflation of the two roads to OA has practical implications and has been holding up OA progress for a decade and a half.

3. The distinction between paid Gold and free Gold is very far from being a straightforward one.

4. Free Gold can be free (to the author) because the expenses of the Gold journal are covered by subscriptions, subsidies or volunteerism.

5. The funds for Paid Gold can come from the author’s pocket, the author’s research grant, the author’s institution or the author’s funder.

6. It would be both absurd and gratuitously confusing to mark each of these economic-model differences with a color-code.

7. Superfluous extra colors would also obscure the role that the colour-code was invented to perform: distinguishing author-side OA provision from publisher-side OA provision.

8. So, please, let’s not have “diamond,” “platinum” and “titanium” OA, despite the metallurgical temptations.

9. They amplify noise instead of pinpointing the signal, just as SHERPA/Romeo‘s parti-colored Blue/Yellow/Green spectrum (mercifully ignored by almost everyone) does.

10. OA is about providing Open Access to peer-reviewed journal articles, not about cost-recovery models for OA publishing (Gold OA).

11. The Gold that publishers are fighting for and that researcher funders are subsidizing (whether “pure” or “hybrid”) is paid Gold, not free Gold.

12. No one knows whether or how free Gold will be sustainable, any more than they know whether or how long subscription publishing can co-exist viably with mandatory Green OA.

13. So please leave the economic ideology and speculation out of the pragmatics of OA policy making by the research community (institutions and funders).

14. Cost-recovery models are the province of publishers (Gold OA).

15. What the research community needs to do is mandate OA provision.

16. The only OA provision that is entirely in the research community’s hands is Green OA.

And, before you ask, please let’s not play into the publishers’ hands by colour-coding OA also in terms of the length of the publisher embargo: 3-month OA, 6-month OA, 12-month-OA, 24-month-OA, millennial OA: OA means immediate online access. Anything else is delayed access. (The only quasi-exception is the “Almost-OA” provided by the author via the institutional repository’s email-eprint-request Button when complying with publisher embargoes — but that too is clearly not OA, which is immediate, free online access.)

And on no account should the genuine, substantive distinction between Gratis OA (free online access) and Libre OA (free online access plus various re-use rights) be color-coded (with a different shade for every variety of CC license)!

Harnad, S., Brody, T., Vallieres, F., Carr, L., Hitchcock, S., Gingras, Y, Oppenheim, C., Stamerjohanns, H., & Hilf, E. (2004) The Access/Impact Problem and the Green and Gold Roads to Open Access. Serials Review 30. Shorter version: The green and the gold roads to Open Access. Nature Web Focus.

Announcing the PLOS Text Mining Collection

Text mining

Post authored by Casey M. Bergman, Lawrence E. Hunter, Andrey Rzhetsky

Text Mining is an interdisciplinary field combining techniques from linguistics, computer science and statistics to build tools that can efficiently retrieve and extract information from digital text. Over the last few decades, there has been increasing interest in text mining research because of the potential commercial and academic benefits this technology might enable. However, as with the promises of many new technologies, the benefits of text mining are still not clear to most academic researchers.

This situation is now poised to change for several reasons. First, the rate of growth of the scientific literature has now outstripped the ability of individuals to keep pace with new publications, even in a restricted field of study. Second, text-mining tools have steadily increased in accuracy and sophistication to the point where they are now suitable for widespread application. Finally, the rapid increase in availability of digital text in an Open Access format now permits text-mining tools to be applied more freely than ever before.

To acknowledge these changes and the growing body of work in the area of text mining research, today PLOS launches the Text Mining Collection, a compendium of major reviews and recent highlights published in the PLOS family of journals on the topic of text mining. As one of the major publishers of the Open Access scientific literature, it is perhaps no coincidence that research in text mining in PLOS journals is flourishing. As noted above, the widespread application and societal benefits of text mining is most easily achieved under an Open Access model of publishing, where the barriers to obtaining published articles are minimized and the ability to remix and redistribute data extracted from text is explicitly permitted. Furthermore, PLOS is one of the few publishers who is actively promoting text mining research by providing an open Application Programming Interface to mine their journal content.

Text Mining in PLOS

Over the years, PLOS has published several reviews, opinions, tutorials and dozens of primary research articles in this area in PLOS Biology, PLOS Computational Biology and, increasingly, PLOS ONE. Because of the large number of text mining papers in PLOS journals, we are only able to highlight a subset of these works in the first instance of the PLOS Text Mining Collection. These include major reviews and tutorials published over the last decade [1-6], plus a selection of research papers from the last two years [7-19] and three new papers arising from the call for papers for this collection [20-22].

The research papers included in the collection at launch provide important overviews of the field and reflect many exciting contemporary areas of research in text mining, such as:

  • methods to extract textual information from figures [7];
  • methods to cluster [8] and navigate [15] the burgeoning biomedical literature;
  • integration of text-mining tools into bioinformatics workflow systems [9];
  • use of text-mined data in the construction of biological networks [10];
  • application of text-mining tools to non-traditional textual sources such as electronic patient records [11] and social media [12];
  • generating links between the biomedical literature and genomic databases [13];
  • application of text-mining approaches in new areas such as the Environmental Sciences [14] and Humanities [16-17];
  • named entity recognition [18];
  • assisting the development of ontologies [19];
  • extraction of biomolecular interactions and events [20-21]; and
  • assisting database curation [22].

 Looking Forward

As this is a living collection, it is worth discussing two issues we hope to see addressed in articles that are added to the PLOS text mining collection in the future: scaling up and opening up. While application of text mining tools to abstracts of all biomedical papers in the MEDLINE database is increasingly common, there have been remarkably few efforts that have applied text mining to the entirety of the full text articles in a given domain, even in the biomedical sciences [4][23]. Therefore, we hope to see more text mining applications scaled up to use the full text of all Open Access articles. Scaling up will maximize the utility of text-mining technologies and the uptake by end users, but also demonstrate that demand for access to full text articles exists by the text mining and wider academic communities.

Likewise, we hope to see more text-mining software systems made freely or openly available in the future. As an example of the state of affairs in the field, only 25% of the research articles highlighted in the PLOS text mining collection at launch provide source code or executable software of any kind [13, 16, 19, 21]. The lack of availability of software or source code accompanying published research articles is, of course, not unique to the field of text mining. It is a general problem limiting progress and reproducibility in many fields of science, which authors, reviewers and editors have a duty to address. Making release of open source software the rule, rather than the exception, should further catalyze advances in text mining, as it has in other fields of computational research that have made extremely rapid progress in the last decades (such as genome bioinformatics).

By opening up the code base in text mining research, and deploying text-mining tools at scale on the rapidly growing corpus of full-text Open Access articles, we are confident this powerful technology will make good on its promise to catalyze scholarly endeavors in the digital age.

To view all the articles or read more about this collection, please visit: The PLOS Text Mining Collection (2013)

Citations:

1.   Dickman S (2003) Tough mining: the challenges of searching the scientific literature. PLoS biology 1: e48. doi:10.1371/journal.pbio.0000048.

2.   Rebholz-Schuhmann D, Kirsch H, Couto F (2005) Facts from Text—Is Text Mining Ready to Deliver? PLoS Biol 3: e65. doi:10.1371/journal.pbio.0030065.

3.   Cohen B, Hunter L (2008) Getting started in text mining. PLoS computational biology 4: e20. doi:10.1371/journal.pcbi.0040020.

4.   Bourne PE, Fink JL, Gerstein M (2008) Open access: taking full advantage of the content. PLoS computational biology 4: e1000037+. doi:10.1371/journal.pcbi.1000037.

5.   Rzhetsky A, Seringhaus M, Gerstein M (2009) Getting Started in Text Mining: Part Two. PLoS Comput Biol 5: e1000411. doi:10.1371/journal.pcbi.1000411.

6.   Rodriguez-Esteban R (2009) Biomedical Text Mining and Its Applications. PLoS Comput Biol 5: e1000597. doi:10.1371/journal.pcbi.1000597.

7.   Kim D, Yu H (2011) Figure text extraction in biomedical literature. PloS one 6: e15338. doi:10.1371/journal.pone.0015338.

8.   Boyack K, Newman D, Duhon R, Klavans R, Patek M, et al. (2011) Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches. PLoS ONE 6: e18029. doi:10.1371/journal.pone.0018029.

9.   Kolluru B, Hawizy L, Murray-Rust P, Tsujii J, Ananiadou S (2011) Using workflows to explore and optimise named entity recognition for chemistry. PloS one 6: e20181. doi:10.1371/journal.pone.0020181.

10.       Hayasaka S, Hugenschmidt C, Laurienti P (2011) A network of genes, genetic disorders, and brain areas. PloS one 6: e20907. doi:10.1371/journal.pone.0020907.

11.       Roque F, Jensen P, Schmock H, Dalgaard M, Andreatta M, et al. (2011) Using electronic patient records to discover disease correlations and stratify patient cohorts. PLoS computational biology 7: e1002141. doi:10.1371/journal.pcbi.1002141.

12.       Salathé M, Khandelwal S (2011) Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control. PLoS Comput Biol 7: e1002199. doi:10.1371/journal.pcbi.1002199.

13.       Baran J, Gerner M, Haeussler M, Nenadic G, Bergman C (2011) pubmed2ensembl: a resource for mining the biological literature on genes. PloS one 6: e24716. doi:10.1371/journal.pone.0024716.

14.       Fisher R, Knowlton N, Brainard R, Caley J (2011) Differences among major taxa in the extent of ecological knowledge across four major ecosystems. PloS one 6: e26556. doi:10.1371/journal.pone.0026556.

15.       Hossain S, Gresock J, Edmonds Y, Helm R, Potts M, et al. (2012) Connecting the dots between PubMed abstracts. PloS one 7: e29509. doi:10.1371/journal.pone.0029509.

16.       Ebrahimpour M, Putni?š TJ, Berryman MJ, Allison A, Ng BW-H, et al. (2013) Automated authorship attribution using advanced signal classification techniques. PLoS ONE 8: e54998. doi:10.1371/journal.pone.0054998.

17.       Acerbi A, Lampos V, Garnett P, Bentley RA (2013) The Expression of Emotions in 20th Century Books. PLoS ONE 8: e59030. doi:10.1371/journal.pone.0059030.

18.       Groza T, Hunter J, Zankl A (2013) Mining Skeletal Phenotype Descriptions from Scientific Literature. PLoS ONE 8: e55656. doi:10.1371/journal.pone.0055656.

19.       Seltmann KC, Pénzes Z, Yoder MJ, Bertone MA, Deans AR (2013) Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology. PLoS ONE 8: e55674. doi:10.1371/journal.pone.0055674.

20.       Van Landeghem S, Bjorne J, Wei C-H, Hakala K, Pyysal S, et al. (2013) Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization. PLOS ONE 8:  e55814. doi: 10.1371/journal.pone.0055814

21.       Liu H, Hunter L, Keselj V, Verspoor K (2013) Approximate Subgraph Matching-based Literature Mining for Biomedical Events and Relations. PLOS ONE 8: e60954. doi: 10.1371/journal.pone.0060954

22.       Davis A, Weigers T, Johnson R, Lay J, Lennon-Hopkins K, et al. (2013) Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the Comparative Toxicogenomics Database. PLOS ONE 8: e58201. doi: 10.1371/journal.pone.0058201

23.       Bergman CM (2012) Why Are There So Few Efforts to Text Mine the Open Access Subset of PubMed Central? http://caseybergman.wordpress.com/2012/03/02/why-are-there-so-few-efforts-to-text-mine-the-open-access-subset-of-pubmed-central/.

 

 

Read Issue 2:2 of MicrobiologyOpen Now!

MicrobiologyOpenThe latest issue of MicrobiologyOpen is available online now! 12 new articles are fully open access: free to read, download and share.

Below are some recent top articles highlighted by the Editor-in-Chief, Pierre Cornelis:

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Summary: In this review, we synthesize the various methods available for topological mapping of ?-helical integral membrane proteins to provide investigators with a comprehensive reference for choosing techniques suited to their particular topological queries and available resources. 
 
purple_lock_openEmbRS a new two-component system that inhibits biofilm formation and saves Rubrivivax gelatinosus from sinking Anne Soisig Steunou, Sylviane Liotenberg, Marie-Noêlle Soler, Romain Briandet, Valérie Barbe, Chantal Astier and Soufian Ouchane 
 
Summary: Ability of the photosynthetic bacterium Rubrivivax gelatinosus to form biofilm. The EmbRS two-component system inhibits biofilm formation. Growth of the EmbRS mutant results in the formation of conspicuous bacterial veils around the toothpick scaffolds.