Meet PLOS at the Biophysical Society 59th Annual Meeting

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PLOS ONE and PLOS Biology are excited to return to the Biophysical Society’s Annual Meeting. The event will be held at the Baltimore Convention Center located in downtown Baltimore, Maryland. All are encouraged to stop by booth #636 to speak … Continue reading »

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Open Science Codefest

Open Science CodefestThe National Center for Ecological Analysis and Synthesis (NCEAS) at UCSB is co-sponsoring the Open Science Codefest 2014, which aims to bring together researchers from ecology, biodiversity science, and other earth and environmental sciences with computer scientists, software engineers, and developers to collaborate on coding projects of mutual interest.

Do you have a coding project that could benefit from collaboration, or software skills you’d like to share? The codefest will be held from September 2-4 in Santa Barbara, CA.

Inspired by hack-a-thons and organized in the participant-driven, unconference style, the Open Science Codefest is for anyone with an interesting problem, solution, or idea that intersects environmental science and computer programming. This is the conference where you will actually get stuff done – whether that’s coding up a new R module, developing an ontology, working on a data repository, creating data visualizations, dreaming up an interactive eco-game, discussing an idea, or any other concrete collaborative goal that interests a group of people.

Looks like a great program!

PLOS ONE Heads to the Big Easy for the 2013 Meeting of the American Society for Cell Biology

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PLOS ONE is excited for the opportunity to exhibit alongside PLOS Biology at the American Society for Cell Biology’s (ASCB) Annual Meeting in New Orleans from December 14 – 18. This year’s ASCB meeting will be held at the Ernest N. Morial Convention Center and is expected to draw approximately 7,000 cell biology enthusiasts. The conference will feature upwards of 100 scientific sessions and 2500 posters on a plethora of topics within cell biology research.  Additionally, as stated on the ASCB Annual Meeting website, Nobel Laureates Randy Schekman, a PLOS ONE author, and James Rotham will be special guest speakers.

We encourage all conference attendees to stop by booth # 211 on Publisher’s Row to speak with PLOS ONE staff and learn about the journal. We look forward to engaging with PLOS ONE authors—current and prospective alike—as well as reviewers, members of our Editorial Board (Academic Editors) and all others wanting to learn about PLOS ONE and PLOS as a whole. Additionally, Dr. Ines Alvarez-Garcia, a Senior Editor from our sister journal, PLOS Biology, will be at the exhibition booth for a “meet the editor” session from noon – 1 pm on Monday, December 16. Be sure to stop by and say hello. After the conference on the evening of the 16th PLOS ONE will be hosting a mixer for all Academic Editors who are in attendance at the event. Please contact Camron Assadi (cassadi@plos.org) to RSVP.

See you in New Orleans on December 14!

In celebration of all things cell biology, here are some of the most viewed and most cited cell biology-related papers published in PLOS ONE over the past year:

Most Viewed

Citation: Rundqvist H, Augsten M, Strömberg A, Rullman E, Mijwel S, et al. (2013) Effect of Acute Exercise on Prostate Cancer Cell Growth. PLoS ONE 8(7): e67579. doi:10.1371/journal.pone.0067579

Citation: Hanauske-Abel HM, Saxena D, Palumbo PE, Hanauske A-R, Luchessi AD, et al. (2013) Drug-Induced Reactivation of Apoptosis Abrogates HIV-1 Infection. PLoS ONE 8(9): e74414. doi:10.1371/journal.pone.0074414

Citation: Bhasin MK, Dusek JA, Chang B-H, Joseph MG, Denninger JW, et al. (2013) Relaxation Response Induces Temporal Transcriptome Changes in Energy Metabolism, Insulin Secretion and Inflammatory Pathways. PLoS ONE 8(5): e62817. doi:10.1371/journal.pone.0062817

Most Cited

Citation: Xu Y, Ding J, Wu L-Y, Chou K-C (2013) iSNO-PseAAC: Predict Cysteine S-Nitrosylation Sites in Proteins by Incorporating Position Specific Amino Acid Propensity into Pseudo Amino Acid Composition. PLoS ONE 8(2): e55844. doi:10.1371/journal.pone.0055844

Citation: Ohkura M, Sasaki T, Sadakari J, Gengyo-Ando K, Kagawa-Nagamura Y, et al. (2012) Genetically Encoded Green Fluorescent Ca2+ Indicators with Improved Detectability for Neuronal Ca2+ Signals. PLoS ONE 7(12): e51286. doi:10.1371/journal.pone.0051286

Citation: Manikkam M, Tracey R, Guerrero-Bosagna C, Skinner MK (2013) Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations. PLoS ONE 8(1): e55387. doi:10.1371/journal.pone.0055387

Image Credit(2004) Protein Helps Orchestrate Cells’ Fluid Uptake. PLOS Biology 2(9): e318. doi:10.1371/journal.pbio.0020318.

 

PLOS ONE at AGU 2013

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PLOS ONE is excited to participate in the American Geophysical Union’s (AGU) Fall Meeting 2013, held this week in San Francisco’s Moscone Center. Conveniently, Moscone is just down the street from our San Francisco office, so several members of PLOS staff will be in attendance and available to chat with you about the journal. We’re looking forward to meeting both current and potential Academic Editors, reviewers, and of course authors! Please stop by Booth #301 to say hello.

Last week was a very geophysics-oriented one for us, with both the publication of Hansen et al.’s work “Assessing “Dangerous Climate Change”: Required Reduction of Carbon Emissions to Protect Young People, Future Generations and Nature” and with the announcement of our call for papers in a new collection entitled “Responding to Climate Change.” What’s more exciting is that James Hansen will be in attendance at AGU and will be giving a talk today (December 10th) on this topic, in support of taking significant, active measures to reduce fossil fuel emissions.

Last year, at AGU 2012, we were a little bit of an unfamiliar face to many. This year, we hope to continue our conversation with the physical sciences community about our commitment to open access and the publication of sound scientific research in all areas of science and medicine, including geoscience, space science, chemistry, and physics.

After AGU, look out for the PLOS booth again in just a few days at the American Society for Cell Biology!

Image Credit: Detailed view of Arctic Sea Ice in 2007, from NASA Visible Earth.

Spotlight on PLOS ONE’s NeuroMapping and Therapeutics Collection

Collection image.pcol.v02.i17.g001Launched in 2010, the Neuromapping and Therapeutics Collection is a unique collaboration between PLOS ONE and the Society for Brain Mapping and Therapeutics. The Neuromapping and Therapeutics Collection provides a forum for interdisciplinary research aimed at translation of knowledge across a number of fields such as neurosurgery, neurology, psychiatry, radiology, neuroscience, neuroengineering, and healthcare and policy issues that affect the treatment delivery and usage of related devices, drugs, and technologies. The Collection is open to submissions on these topics from any researcher—so far, 24 research papers have been published as part of this Collection.

We spoke to Dr. Allyson Rosen, one of the members of the Society for Brain Mapping and Therapeutics who helps coordinate the Neuromapping and Therapeutics Collection, to discuss the latest news and research in this area, and the new submissions to the collection they’re hoping to see in the next few months:

What’s exciting in Neuromapping and Therapeutics at the moment?

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It is exciting to see how creative scientists and clinicians are at solving important clinical problems by combining diverse techniques in innovative ways. We see our collection as a home for cross-disciplinary work that might not “fit” in traditional journals. For example, we have published MR methods to enable effective brain infusions and work that exploits computer-aided design for cranial reconstructions. There are invasive and non-inva

What are the implications of President Obama’s commitment to Human Brain Mapping research?sive techniques for stimulating selective brain regions and creating focal lesions, such as transcranial magnetic stimulation, transcranial Doppler technology, and X-ray microplanar beam technology. There are also innovative analysis techniques that exploit powerful computational methods that were previously unavailable.

Given the high-profile nature of the Brain Mapping Initiative and the state of the US economy, we have advocated that there be some clinical implications to the announcement. We believe that this approach will ensure continued public support at a time of great need and uncertainty.

Are there any specific research areas where you’d like to see more submissions to the Collection?

We are proud of the work we’ve received and deeply impressed with the broad array of papers submitted so far. This is a testament to the creativity of our contributors, and we welcome their diversity. We particularly welcome work presented at the international meeting of the Society for Brain Mapping and Therapeutics that occurs in the spring of each year.

Why do you think it’s important to publish this kind of research in an open access journal such as PLOS ONE?

Our society is committed to being inclusive and welcoming any profession that seeks to improve the health and wellbeing of patients with brain disorders. An open access journal enables easier promotion of work we feel is important and encourages sharing among diverse disciplines. Often, truly cutting-edge work is so far ahead of its time that there is not yet an appreciation for its importance. Often, clinical problems are seen as practical but not necessarily novel. We appreciate the mission of PLOS ONE as upholding strong scientific integrity and not as triaging work based on arbitrary decisions regarding importance.

To read more about this Collection, including new research papers like, “Verifying three-dimensional skull model reconstruction using cranial index of symmetryandUnique anti-glioblastoma activities of Hypericin are at the crossroad of biochemical and epigenetic events and culminate in Tumor Cell Differentiation,” click here.

Come visit us at SFN 2013.

Both the Society for Brain Mapping and Therapeutics and PLOS ONE will be attending SFN 2013 – please drop by booth #136 to say hello and learn more about the Collection. For instructions on how to submit to the Collection, please visit the Collection page and download the submission document.

If you have any questions about this Collection, or any other PLOS Collections, please email collections@plos.org

Image credit for Collection cover: Alka Joshi

Public Health Links, Lost in Translation

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PLOS is at SpotOn London (#solo13) again this year, taking part in workshops and panels on science communication tools, policy, and outreach. On Friday November 8, I’ll be joined by three PLOS authors and two independent science journalists for a science outreach workshop titled Public Health Links, Lost in Translation. With our moderator, science journalist Suzi Gage (@soozaphone) of the Sifting the Evidence blog on The Guardian, we will address weak links in the science communication “food chain” that contribute to falling vaccination rates, mainly in the UK, Europe, and the US.

For this session, I will be speaking as Editorial Director of PLOS ONE, the world’s largest scientific journal. But the debate around vaccination began before PLOS existed and it has gone on longer than I’ve been involved in science communication. Coming as I do from a background of ‘peddling the evidence,’ it disturbs me when I see evidence ignored in favour of quackery. But I also bring a personal perspective to this issue. As with climate change, it frustrates me that my own actions are not enough to safeguard my children against a threat to their health and safety. Although no vaccine is perfect, every time my children play with others who are intentionally un-vaccinated their risk of contracting preventable contagious diseases increases.

So it seems to me that the aim of this workshop will be to use our combined perspectives – and those of the science community members present – to discuss how we strengthen the links between evidence-based science and the public on vaccines. We aren’t the first and certainly won’t be the last meeting of scientists and science writers to take on this issue, but that doesn’t let us off the hook and excuse us for not trying.

Good and Bad News

The news on vaccines in the UK is not all bad. By summer of 2013, ninety per cent of two-year-old children had received their first dose of the MMR (measles-mumps-rubella) vaccine – the highest level for 13 years according to the Health Protection Agency. This uptake in MMR vaccinations has been a public reaction to widely-reported measles outbreaks in Europe and the UK – suggesting an appropriate public response to highly visible evidence. However, present MMR uptake is still short of the 95% rate that would establish a sufficient level for herd immunity, which would stop the spread of the disease in the community.

The Legacy of MMR

All of us continue to pay the price for the broken public trust that came from the Andrew Wakefield-MMR debacle of the mid-90s. Strong distrust concerning vaccine safety exists not only in rich and middle income countries, but also on the front lines of the Global Polio Eradication Initiative, as my colleagues at PLOS Medicine have covered in depth.

The link between this widespread distrust and falling vaccination rates are clearly established:

New vaccinations for diseases such as HPV, and new approaches to old ones, e.g. targeting different populations to avert new outbreaks of influenza or shingles, increase the challenges for public health practitioners and advocates.

A More Honest System

In many ways, I don’t blame the public for being mistrustful of scientific research – the scientific community and mainstream media make it very hard for people to know what to believe. As Editorial Director of a large journal, I see the entire spectrum of misinterpretation of data. I see original datasets being over-interpreted by authors, in order to get published in top journals. I see journalists taking these papers and adding yet another layer of spin in order to sell them to the public. I see newspaper editors pushing the most shocking articles to the front pages to ensure maximum impact. It’s little wonder that the public are mistrustful.

At PLOS ONE, we are trying to deal with these challenges by encouraging honest reporting of data. By removing the question of ‘novelty’ and ‘impact’ from our review process, we aim to get authors to state simply what they’ve discovered without feeling they have to dress it up in layers of over-interpretation. That drug you’ve discovered kills some cells in a petri dish. Great! Is it a cure for cancer? No. So don’t say it is – we’ll still publish your paper!

We are also very careful about what we release to the press, and how the message is put out. Clearly we can’t stop journalists misinterpreting our papers, but we can at least give the science we publish a decent chance of being reported correctly.

Finally, we track press and blog coverage and add it to the comments of the papers. Combined with our Article-level Metrics, which display a whole array of reactions to the paper and usage statistics, readers can see whether high activity on a paper is a result of heavy media attention, or whether it’s from interest from other researchers.

Certainly the papers most covered in the press are among those that receive the most views, so if we are to affect public attitudes on vaccines or any other highly-charged public health or science issue, we are as dependent on the excellent work of our authors as we are on our colleagues in new and old media. Panelists at this Friday’s SpotOn London 13 workshop represent this wide spectrum. With each bio below, I’ve included some of the research or science writing that will inform our discussion.

Marc Baguelin PhD (@marcbaguelin) is a mathematical modeler working in the Immunisation department at the Health Protection Agency and at the London School of Hygiene and Tropical Medicine on models of influenza transmission, immunization, and control. Marc’s research has been published in the journals Vaccine, Biostatistics, and Emerging Infectious Disease. His latest study, Assessing Optimal Target Populations for Influenza Vaccination Programmes: An Evidence Synthesis and Modelling Study, published in PLOS Medicine, resulted in a change of UK health policy with an extension of the influenza vaccination programme to 2-16 year old children.

Tammy Boyce, PhD (@tamboyce) holds an honorary lecturing post with the Centre for Infection Prevention and Management, Imperial College London, Hammersmith Hospital, London, and was a Research Fellow in Health, Risk, Science and Communication at the Cardiff School of Journalism.  Tammy’s research has been published in Nature Reviews Immunology, and the British Journal of Healthcare Management. She was one of the first to examine public reception of media coverage and the impact the style of reporting has on public opinion and vaccination decisions. From this research, Tammy published the book Health, Risk and News: The MMR Vaccine and the Media (with Peter Lang, 2007). Her latest research article in PLOS ONE examines the role of the school nurse in addressing inequities in HPV vaccine uptake in the UK.

Stephan Lewandowsky PhD (@STWorg) is a cognitive scientist in the School of Experimental Psychology, University of Bristol, UK. His research, published in Nature Climate Change, Journal of Experimental Psychology, and Cognitive Psychology, examines peoples’ memory and decision making with particular emphasis on how people respond to corrections of misinformation. His latest PLOS ONE research article, The Role of Conspiracist Ideation and Worldviews in Predicting Rejection of Science,. studies how conspiracist thinking affects public attitudes towards scientific issues; as Hilda Bastain blogged: a “strong consensus around science can be seen as evidence that ‘they’re all in cahoots’… with vaccination, say, presenting yet more facts or another study could paradoxically confirm their rejection of science.”

Beth Skwarecki (@BethSkw) is an independent science journalist specializing in public health issues who writes for AAAS Science News, and DoubleXScience and blogs on the PLOS BLOGS Network. Recent posts have covered the HPV vaccine’s “image problem” and the role of Twitter in spreading misinformation on the 2009 H1N1 pandemic.

Please add your thoughts and suggest questions for our panel by tweeting to the hashtag #solo13links. You can watch the live stream of the discussion at: http://plos.io/solo13links

Here is the entire Spot On London 2013 program, FYI. Keep in mind all sessions will be live streamed with the archives kept online thereafter for your viewing.

The New PLOS ONE Collection on “Sauropod Gigantism – A Cross-Disciplinary Approach”

Sauropod-Collection-600x600 (3) (2)The exceptional gigantism of sauropod dinosaurs has long been recognized as an important stage in the evolution of vertebrates, the presence of which raises questions as to why no other land-based lineage has ever reached this size, how these dinosaurs functioned as living animals, and how they were able to maintain stable populations over distinct geological periods.

We are pleased to announce the publication of a PLOS Collection featuring new research on the complex Evolutionary Cascade Theory that attempts to answer  these questions and  explain how the unique gigantism of sauropod dinosaurs was possible. The fourteen papers that make up the collection address sauropod gigantism from a number of varied disciplinary viewpoints, including ecology, engineering, functional morphology, animal nutrition, evolutionary biology, and paleontology.

Sauropod dinosaurs were the largest terrestrial animals to roam the earth, exceeding all other land-dwelling vertebrates in both mean and maximal body size. While convergently evolving many features seen in large terrestrial mammals, such as upright, columnar limbs and barrel-shaped trunks, sauropods evolved some unique features, such as the extremely long necks and diminutive heads they are famous for. Dr Martin Sander, Professor of Paleontology at Universität Bonn and coordinating author for this series of 14 papers, said of the collection:

“This new collection brings together the latest research on the biology of sauropod dinosaurs, the largest animals to ever walk on Earth. Having been extinct for 65 million years, reconstructing sauropod biology represents a particular challenge. Using a wide array of scientific expertise, often from seemingly unlikely fields, has led to some amazing insights. For example, principles of soil mechanics have been used to ‘weigh a dinosaur’ based on its trackways, whilst the latest in computer modeling can make a dinosaur walk again.

The ultimate question underlying this research is how sauropods were able to evolve their uniquely gigantic body size. The wide-ranging disciplines covered in the collection means that there is a -broad, multi-disciplinary audience for the research, as well as general interest in dinosaurs; therefore, we felt that it was essential to publish such a volume in a leading open-access journal such as PLOS ONE to ensure the widest possible dissemination of our work.”

Readers are able to download “Sauropod Gigantism: A Cross-Disciplinary Approach” not only as a PDF but also as an ebook (.mobi and .epub formats) from the collection page. It will also be available on Flipboard (search “PLOS Collections”).

www.ploscollections.org/sauropodgigantism

Image credits:
Collection Image: Kent A. Stevens, University of Oregon

The RosettaCon 2012 Collection: Rosetta Developers Meet the Challenges in Macromodeling Head On

Rosetta2012 Collection ImageReproducibility continues to be one of the major challenges facing computational biologists today. Complicated experiments, massive data sets, scantily described protocols, and constantly evolving code can make experimental documentation and replication very difficult.  In addition, the need for specialized knowledge and access to large computational resources can create barriers when trying to design and model macromolecules.

Every year, the Rosetta developer community meets to discuss these challenges and advancements via Rosetta, a software suite that models and helps design macromolecules. In 2010, PLOS announced the RosettaCon2010 Collection, which made the latest research on protocols used to create macromolecular models available to all. Now, the PLOS ONE RosettaCon 2012 Collection continues to tackle issues related to use, reproducibility and documentation by highlighting new scientific developments within the Rosetta community.

The RosettaCon 2012 Collection comprises 14 articles detailing the scientific advancements made by developers that use Rosetta. In order to address reproducibility and documentation challenges, each article within this Collection includes an archive containing links to the exact version of the code used in the paper, all input data, links to external tools and example scripts.

This year’s Collection marks the tenth anniversary of RosettaCon and focuses on three long-term goals of the community: increase the usability of Rosetta, improve its current methods, and introduce completely new protocols.

Increasing the usability of Rosetta – Rosetta still requires specialized knowledge and large computational resources, but this collection features two articles describing advancements that make it easier for non-experts to use its applications. These articles introduce the Rosetta Online Server that Includes Everyone (ROSIE) workflow, which allows for rapid conversion of Rosetta applications into public web servers, and PyRosetta, a new graphical user interface (GUI) which allows users to run standard Rosetta design tasks.

Improving current prediction methods – Several articles describe improvements to Rosetta’s structure prediction capabilities and design methodologies. Some examples include improvements to loop conformational sampling, and a recently developed ray-casting (DARC) method for small molecule docking now enables virtual screening of large compound libraries.

Introducing new protocols – A number of articles featuring new procedures and applications that debuted at the conference are introduced in the Collection. Highlights include new methods for dealing with ligand docking, advancements to pre-refine scaffold proteins prior to computational design of functional sites, and new protocols to drive Rosetta de novo modeling.

The RosettaCon 2012 Collection continues to help serve the Rosetta community in an effort to ensure that newly developed protocols are as usable as more established workflows, are transparent, and are accurately documented even in an active development environment.

This post has been adapted from “The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone” which serves as a more in-depth overview of the new collection. To read all that this Collection has to offer, click here.

ISMB/ECCB 2013: much ado about data sharing

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Last month PLOS ONE attended the ISMB/ECCB 2013 conference in Berlin on Intelligent Systems for Molecular Biology. More than 1,500 delegates attended what is the largest conference on computational biology in the world to discuss the latest developments in computational methods that address biological questions.

The opening keynote from PLOS ONE Academic Editor Gil Ast focused on alternative splicing, a mechanism by which several mRNA transcripts are generated from the same mRNA precursor, thus enhancing transcriptome and proteome diversity. He mentioned a paper his group published earlier this year in PLOS ONE, in which they showed that pre-mRNA splicing influences nucleosome organization, suggesting that there is a bi-directional interplay between chromatin organization and splicing. While it is widely accepted that chromatin organization and DNA modification regulate transcription, it is intriguing that splicing can in turn affect chromatin organization, and this may constitute an additional layer of regulation of gene expression. He also presented exciting recent findings showing how pre-mRNA splicing and the creation of new exons in the human genome may be linked to certain genetic disorders and types of cancers.

Picture1 Understanding the biology of complex human disease is also one of Goncalo Abecasis’s objectives, winner of the ISCB 2013 Overton Prize. Specifically, he is interested in better understanding genetic variation and its connections to human diseases using computational methods and statistical tools. In his talk, he emphasized that the identification and characterization of the genetic variants that affect human traits may be achieved by examining the link between these traits and the complete genome sequences of thousands of individuals. To collect DNA from as many people as possible, he wondered whether we should make use of social media to call for volunteers to send their DNA samples. Are Facebook and Twitter the key to understanding human genetics?

One topic that generated much discussion at the meeting was data sharing. In her talk, Carole Goble called for all scientists to share their data widely as to enable reproducibility, a principle underpinning the scientific method.  Several journals, including PLOS ONE, require that all data (including all relevant raw data) described in the manuscript be made freely available to any scientist wishing to use them for the purpose of academic, non-commercial research. Well established and widely supported public repositories already exist for certain types of data such as nucleic acid sequences, and in cases where an appropriate repository does not exist, there are also general data repositories such as Dryad. Assigned accession numbers or digital object identifiers (DOIs) facilitate data citation and ensure accountability. An increasing number of research funding agencies also now support data sharing in the life sciences. Whilst there is indeed increasing discussion to make primary data from published research publicly available, Goble mentioned a paper by Ioannidis and colleagues showing that a substantial proportion of articles published in high-impact journals do not comply (or only weakly comply) with data availability requirements. According to Goble, a lack of data sharing, and thus reproducibility, could lead to an increase in retracted scientific papers.

She also urged the computational biology community to release their “dark data”, i.e. data that is not published and remains hidden on various USB drives and computers, the point being that if shared more people will be able to use these results, increasing visibility, accountability and reproducibility. As highlighted by a recent study, data sharing is not an end in itself, but rather a crucial form of scientific knowledge dissemination.

 

Citations:

Keren-Shaul H, Lev-Maor G, Ast G (2013) Pre-mRNA Splicing Is a Determinant of Nucleosome Organization. PLoS ONE 8(1): e53506. doi:10.1371/journal.pone.0053506

Alsheikh-Ali AA, Qureshi W, Al-Mallah MH, Ioannidis JPA (2011) Public Availability of Published Research Data in High-Impact Journals. PLoS ONE 6(9): e24357. doi:10.1371/journal.pone.0024357

Wallis JC, Rolando E, Borgman CL (2013) If We Share Data, Will Anyone Use Them? Data Sharing and Reuse in the Long Tail of Science and Technology. PLoS ONE 8(7): e67332. doi:10.1371/journal.pone.0067332

Images:

Wikimedia by Angelineri

Modified from Schwartz S, Oren R, Ast G (2011) Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads. PLoS ONE 6(1): e16685. doi:10.1371/journal.pone.0016685

 

Announcing the Ecological Impacts of Climate Change Collection

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Post authored by Collection Curator Ben Bond-Lamberty 

The ecological impacts of climate change are broad and diverse, and include alterations to species’ range limits, plant phenology and growth, carbon and nutrient cycling, as well as biodiversity and extinction risk. Recent PLOS articles have used a variety of experimental and observational approaches to examine these subjects.

Identifying at-risk regions, taxa, and species is a critical first step in adaptation and conservation efforts. A study by Mouillot et al. suggested that rare species are particularly important in conservation efforts, as rare species in diverse ecosystems are not replaceable by other species that fulfill the same ecological functions. At the same time, both rare and more common species experience the ecological impacts of climate change. Foden et al. combined biology and ecology to assess, on a global scale, the climate change vulnerability of birds, amphibians, and corals based on expert assessment and literature surveys. In a more regionally focused study, Gardali et al. assessed climate-change risk for California’s vulnerable bird species.

Birds were also the focus of two studies documenting how particular species can be ‘winners’ or ‘losers’ in a changing climate. Receding glaciers and thus increased breeding habitat have led to population increases for Adélie penguins in the southern Ross Sea. The outlook was more mixed for Pacific western grebes , which have shifted south, perhaps in response to changes in their forage fish prey. Further down the food chain, Suikkanen et al.  used thirty years of marine data to infer that climate change and eutrophication drove a trophic shift in Baltic Sea food webs.

Long-term data were also used to study how flowering dates have changed since the mid-19th century. In a study that received extensive media coverage, Ellwood et al. used flowering records initiated as early as 1852 to show that high spring temperatures in 2010 and 2012 resulted in the earliest flowering in recorded history in the eastern United States. The biological pathways through which temperature affects seasonal timing in endotherms were discussed by Caro et al. Two other widely-covered studies focused on coffee: predicting future trends and identifying priorities, and climate change impacts on this plant and one of its important pests. Both examine adaptation possibilities for managing coffee crops over the coming century.

Adaptation and vulnerability were central themes for Guest et al., who reported that corals under thermal stress showed lower bleaching susceptibility at locations that bleached a decade earlier, implying an adaptive or acclimatization response. The molecular mechanisms behind such thermal tolerance were explored by Bellantuono et al.

Finally, the ecological impacts of climate change affect our health, the urban environment, and the agricultural economy. Airborne pollen counts have been increasing across Europe, and Ziello et al. suggest that rising CO2 levels may be influencing this increase. In another study, Meineke et al. used an elegant combination of observation and manipulative experiments to show that urban warming was a key driver of insect pest outbreaks in the southeastern U.S. Rising temperatures are a significant driver for the expanding range of Asian tiger mosquitoes, known vectors for West Nile and other viral infections. Warming was also found to contribute to the decreasing quality of grassland for grazers such as bison and cattle, although the effects are often exerted via complex interactions with other factors.

The broad range of these papers emphasize not only the multi-faceted impacts of climate change on ecological and human systems, but also the breadth and depth of research on these subject being reported in the PLOS journals. These journals seem a particularly appropriate venue for the ‘citizen science’ and other long-term data used by many of these studies.

Collection Citation: Ecological Impacts of Climate Change Collection (2013) http://www.ploscollections.org/ecoclimatechange

Image Credit: (Clockwise from top) William Warby. Flickr.com. Thomas Vignaud. PLOS Biology. 2011. 9(4). Colombi et al. PLOS ONE. 2013. Soto-Azat et al. PLOS ONE. 2013.

This Collection is also available on Flipboard, please search “PLOS Collections” to subscribe.

 

A Bechdel test for scientific workshops

After attending two recent scientific conferences, one which was gender balanced, and one which was so gender-imbalanced that it engendered snarky out-of-band twitter comments, it struck me that we might need a Bechdel Test for scientific workshops.  The Bechdel test is a simple test for movies.  To pass the test, a movie has to have:

  1. at least two [named] women in it,
  2. who talk to each other,
  3. about something besides a man.

Seems simple, right?  You’d be amazed at just how few popular movies pass the test, including some set in universes that were originally designed for equality. (I’m talking about you, Star Trek reboot.)

Here’s an analogous test for scientific workshops or conference symposia.  Does the workshop have:

  1. at least two female invited speakers,
  2. who are asked questions by female audience members,
  3. about their research.

Again, this seems simple, right?  But you’d be shocked how few scientific conference symposia or workshops can live up to this standard.  I suspect this depends strongly on specific research fields. 

Rigoberto Hernandez has been talking about advancing science through diversity for quite a while.  I finally got to hear him speak about the OXIDE project on this latest trip, and he’s got a lot of great things to say about how diversity can strengthen science. I think one great way to help is to point out the good conferences we attend which live up to this standard.

Rigoberto also happened to be one of the organizers of the gender-balanced conference, which was also one of the best meetings I’ve ever attended.

Meet PLOS ONE at ISMB/ECCB 2013 in Berlin

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Next week PLOS ONE will join PLOS Computational Biology at the ISMB/ECCB 2013 International Society for Computational Biology meeting held this year in Berlin, Germany, July 21-23.

The world’s largest bioinformatics/computational biology conference will bring together scientists from computer science, molecular biology, mathematics, statistics and other related fields to discuss the development and application of computational methods for biological questions. Keynote speakers include David Eisenberg, Gary Stormo, Lior Pachter, and PLOS ONE Academic Editor Gil Ast.

Whether you are interested in joining our Editorial Board or just want to talk about the journal or open access in general, please stop by the PLOS booth (booth #13)!

Academic Editors: If you are also attending, please get in touch ahead of the meeting with Associate Editor Christna Chap to schedule a meeting.

We hope to see you in Berlin!

 

Image: Salipante SJ, Sengupta DJ, Rosenthal C, Costa G, Spangler J, et al. (2013) Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections. PLoS ONE 8(5): e65226. doi:10.1371/journal.pone.0065226

Moms and babies respond to childbirth with different stress hormones

stress

A quick internet search reveals that many women rank giving birth as one of the most painful human experiences. Though pain can be hard to quantify objectively, the physiological stress of childbirth is clinically assessed by measuring blood levels of the stress hormone cortisol.

Cortisol is currently used to estimate the stress experienced by both mother and child during the process of giving birth, but recently published PLOS ONE research suggests that a different stress hormone, corticosterone, may be a more accurate way to measure the stress experienced by healthy, full-term babies.

For their study, researchers tested fetal levels of cortisol and corticosterone in 265 samples of umbilical cord blood from healthy deliveries. Though the total levels of cortisol detected were higher than corticosterone levels, fetuses produced the latter at a greater rate in response to the stress of labor and delivery. Newborns secreted more corticosterone when a Caesarian section was performed due to complications during labor than they did after a normal C-section. Fetal corticosterone levels were also higher after passage through the birth canal. These differences were not seen in levels of cortisol production. Based on these data, the authors suggest that the full-term fetus is more likely to secrete corticosterone than cortisol in response to stress and hence, corticosterone may be a more accurate clinical biomarker to assess fetal stress.

Corticosterone isn’t unheard of in the adult world, as adults continue to make the hormone throughout our lives, though in a much smaller proportion relative to cortisol. When babies switch to producing more cortisol rather than corticosterone isn’t yet clear, but the developmental changes involved may help track or diagnose adrenal gland functions in newborns.

Citation: Wynne-Edwards KE, Edwards HE, Hancock TM (2013) The Human Fetus Preferentially Secretes Corticosterone, Rather than Cortisol, in Response to Intra-Partum Stressors. PLoS ONE 8(6): e63684. doi:10.1371/journal.pone.0063684

Image: stress by topgold

On Reproducibility

I just got back from a fascinating one-day workshop on “Data and Code Sharing in Computational Sciences” that was organized by Victoria Stodden of the Yale Internet Society Project. The workshop had a wide-ranging collection of contributors including representatives of the computational and data-driven science communities (everything from Astronomy, and Applied Math to Theoretical Chemistry and Bioinformatics), intellectual property lawyers, the publishing industry (Nature Publishing Group and Seed Media, but no society journals), foundations, funding agencies, and the open access community. The general recommendations of the workshop are going to be closely aligned with open science suggestions, as any meaningful definition of reproducibility requires public access to the code and data.

There were some fascinating debates at the workshop on foundational issues; What does reproducibility mean? How stringent of a reproducibility test should be required of scientific work? Reproducible by whom? Should resolution of reproducibility problems be required for publication? What are good roles for journals and funding agencies in encouraging reproducible research? Can we agree on a set of reproducible science guidelines which we can encourage our colleagues and scientific communities to take up?

Each of the attendees was asked to prepare a thought piece on the subject, and I’ll be breaking mine down into a couple of single-topic posts in the next few days / weeks.

The topics are roughly:

  • Being Scientific: Fasifiability, Verifiability, Empirical Tests, and Reproducibility
  • Barriers to Computational Reproducibility
  • Data vs. Code vs. Papers (they aren’t the same)
  • Simple ideas to increase openness and reproducibility

Before I jump in with the first piece, I thought it would be helpful to jot down a minimal idea about science that most of us can agree on, which is “Scientific theories should be universal”. That is, multiple independent scientists should be able to subject these theories to similar tests in different locations, on different equipment, and at different times and get similar answers. Reproducibility of scientific observations is therefore going to be required for scientific universality. Once we agree on this, we can start to figure out what reproducibility really means.