Author Archives: plos

Facilitated Preprint Posting is now available for Lab Protocols at PLOS ONE

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Author: Marcel LaFlamme, Open Research Manager, PLOS

When authors submit a Lab Protocol to PLOS ONE, they prepare a short manuscript that contextualizes their step-by-step protocol, describing the value it adds to the published literature and providing evidence that the protocol works. This additional context helps readers to decide whether and, if so, how to adapt the protocol for their own research.

In 2023, PLOS is making it easier for authors to share these protocol manuscripts as preprints, by expanding our partnership with the preprint server bioRxiv to include Lab Protocols.

During the submission process, Lab Protocol authors will now be asked if they want PLOS to forward their manuscript to bioRxiv to be considered for public posting within a few days. Facilitated posting to bioRxiv has been offered at PLOS ONE since 2018. Extending this service to Lab Protocols means that authors can share and get credit for their methods development work sooner, even as the peer review process unfolds.

In keeping with PLOS ONE’s multidisciplinary scope, Lab Protocol submissions are welcomed from any scientific field. Through the end of 2022, 61% of submitted Lab Protocols were in the life sciences, making bioRxiv an especially suitable partner to promote their early sharing.

“bioRxiv has always encouraged authors to post new methods as preprints,” said Richard Sever, co-founder of bioRxiv. “Formats like Lab Protocols that put protocols in context and provide data supporting their use are a great way to make methods more discoverable, and we’re delighted to partner with PLOS to make these manuscripts immediately available to researchers.”

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Protocol entry service expanded to all Lab Protocol authors

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Author: Marcel LaFlamme, Open Research Manager, PLOS

When it comes to methods sharing, Lab Protocols at PLOS ONE offer researchers the best of both worlds: a platform specifically designed for step-by-step protocols, and a peer-reviewed publication in a well-regarded journal.

As of today, we are expanding a service offered to Lab Protocol authors through our partnership with protocols.io: the team at protocols.io will format step-by-step protocols for their platform at no charge and at any stage of the Lab Protocol writing or review process, even prior to submission.

This service will save time for PLOS ONE authors who may not be familiar with the rich functionality of the protocols.io platform, which includes features like timers, labels for critical steps, and the option to embed media objects like videos. The team at protocols.io can also provide feedback to help authors improve the protocol’s presentation, clarity, and reproducibility.

“One of the things I love about Lab Protocols is that they help researchers get credit for method development and publish sooner in their careers. Now, with the expansion of the protocol entry service, we are going a step further in making researchers’ lives easier. I am really excited about this expansion and believe that it is a unique offering in the protocol publishing space,” said Lenny Teytelman, CEO of protocols.io.

Previously, the protocol entry service was offered to Lab Protocol authors whose submissions had already been sent out for peer review. By expanding it to all current and future Lab Protocol authors, PLOS ONE is making it easier for authors to provide an optimized step-by-step protocol as part of their initial submission.

Authors also have complete control over how and when the protocol is made available at protocols.io. The newly formatted protocol will not be visible to anyone else until the author has been able to inspect it and make changes. Authors can then choose to share it publicly, or to generate a private link accessible only to PLOS ONE editors and reviewers. In the event that the Lab Protocol is not accepted at PLOS ONE, authors can still choose to share the step-by-step protocol on protocols.io for other researchers to use and build on.

Lab Protocol authors can access this free service by emailing plosone@plos.org to request a customer code, which will be provided in two to three business days. The author can then enter the code when submitting their step-by-step protocol to the protocol entry service.

“We are delighted that the team at protocols.io is now offering this service to all Lab Protocol authors. Helping authors make the most of the unique features of the protocols.io platform will ensure that the protocol is widely used, shared and further developed. This service is very much aligned with our goal of making the submission process as painless and straightforward for our authors as possible,” said Emily Chenette, Editor in Chief of PLOS ONE.

Image credit: protocols.io

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Conference-ing in a Virtual World

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This blog was written by Nancy Beam, Senior Editor, PLOS ONE

AIDS 2020: Virtual, the 23rd International AIDS Conference hosted by the International AIDS Society, may portend the future of international conferences regardless of when the COVID-19 pandemic is brought under control. AIDS 2020 was originally planned to take place in San Francisco and Oakland, California from July 6-10. This two-city format, itself a revolutionary innovation, was meant to highlight the health disparities and innovative responses to HIV/AIDS of these two iconic cities. The organizers then switched to a completely virtual format in late March in response to the COVID-19 pandemic.

The virtual conference provided many advantages. The conference registration fees were greatly reduced. Travel, lodging, and poster-printing costs were eliminated. Travel hassles and jetlag did not decrease attendees’ ability to focus. Although the International AIDS Conference has always provided a platform for people living with HIV, community organizers, providers, and researchers to contribute, this conference seemed particularly suited to weaving different perspectives together. For example, Prime Sessions combined presentations by scientific experts on a topic with talks by community advocates about their work and lived experiences. Up-to-date findings were easily integrated into the conference program, and a free COVID-19 conference was added to the AIDS 2020 conference only two months before it was scheduled to begin.

Conversely, I missed the excitement of travel, meeting new people, and the atmosphere of exhilaration created by being in the same room with a large group of people. I missed running into old colleagues from the HIV/AIDS community and serendipitous conversations struck up while waiting in line or for presentations to start, or while gathered around a poster. While there were public chat forums meant to encourage these types of conversations, I didn’t find any substantive conversations going on there. Finally, I opted out of browsing through the exhibitions. Without the smell of fresh popcorn, the lure of free lattes, and the possibility of stocking up on the ubiquitous free pens, so beloved at last year’s conference, I didn’t wander through the exhibit booths on my way to somewhere else. I saw pop-up invites to talks and gatherings at booths, so I may have missed out on some engagement opportunities. Even at a virtual conference, there is still too much to do

Predictably, technical problems occurred and while travel barriers were eased, internet access remained a barrier for some participants especially for those who could not access their offices. In addition, because they weren’t traveling, some attendees reported that they were expected to continue working, making it difficult to attend sessions. While conference sessions will be available online for a month after the conference, the expectation that participants continue adding webinar viewing to their workday is a heavy burden. My expectation was that virtual attendance would increase the diversity of attendance as travel and cost barriers were decreased, but without seeing the data, I am not able to judge whether this occurred, or if work and internet access presented too great a barrier. I look forward to hearing what IAS reports about the impact on diversity.

I personally found the tech support to be quick and helpful. However, some website features were surprisingly unsophisticated. For example, the search function only allowed searching for one keyword at a time. So, searching for posters with the keyword “transgender” was quite specific, but “drug delivery systems” produced far too many false positives. Also, searches couldn’t be saved, so after viewing one poster or presentation on a topic, the search had to be rerun. I would have also liked to have been able to click on links in the conference program to go directly to sessions rather than having to navigate to sessions through a separate listings.

As with working remotely, having learned from this forced experiment the pros and cons of a virtual conference, the conferences of the future are likely to be different, and better, than before. A blend or virtual and in-person participation will make for a richer, more diverse, more accessible experience for all.

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Filling in the Scientific Record: The Importance of Negative and Null Results

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PLOS strives to publish scientific research with transparency, openness, and integrity. Whether that means giving authors the choice to preregister their study, publish peer review comments, or diversifying publishing outputs; we’re here to support researchers as they work to uncover and communicate discoveries that advance scientific progress. Negative and null results are an important part of this process. 

This is something we agree on across our journal portfolio — the most recent updates from PLOS Biology being one example– and it’s something we care about especially on PLOS ONE. Our journal’s mission is to provide researchers with a quality, peer-reviewed and Open Access venue for all rigorously conducted research, regardless of novelty or impact. Our role in the publishing ecosystem is to provide a complete, transparent view of scientific literature to enable discovery. While negative and null results can often be overlooked — by authors and publishers alike — their publication is equally as important as positive outcomes and can help fill in critical gaps in the scientific record. 

 

We encourage researchers to share their negative and null results.

 

To provide checks and balances for emerging research 

Positive results are often viewed as more impactful. From authors, editors, and publishers alike, there is a tendency to favor the publication of positive results over negative ones and, yes, there is evidence to suggest that positive results are more frequently cited by other researchers. 

Negative results, however, are crucial to providing a system of checks and balances against similar positive findings. Studies have attempted to determine to what extent the lack of negative results in scientific literature has inflated the efficacy of certain treatments or allowed false positives to remain unchecked. 

The effect is particularly dramatic in meta-analyses which are typically undertaken with the assumption that the sample of retrieved studies is representative of all conducted studies:

 

“However, it is clear that a positive bias is introduced when studies with negative results remain unreported, thereby jeopardizing the validity of meta-analysis (25, 26). This is potentially harmful as the false positive outcome of meta-analysis misinforms researchers, doctors, policymakers and greater scientific community, specifically when the wrong conclusions are drawn on the benefit of the treatment.”

— Mlinari?, et al (2017). Dealing with publication bias: why you should really publish your negative results. Biochem Med (Zagreb) 27(3): 030201

 

As important as it is to report on studies that show a positive effect, it is equally vital to document instances where the same processes were not effective. We should be actively reporting, evaluating, and sharing negative and null results with the same emphasis we give to positive outcomes.

 

To reduce time and resources needed for researchers to continue investigation

Regardless of the outcomes, new research requires time and financial resources to complete. At the end of the process, something is learned — even if the answer is unexpected or less clear than you had hoped for. Nevertheless, these efforts can provide valuable insights to other research groups.

If you’re seeking the answer to a particular scientific question, chances are that another research group is looking for that answer as well: either as a main focus or to provide additional background for a different study. Independent verification of the results through replication studies are also an important piece of solidifying the foundation of future research. This also can only happen when researchers have a complete record of previous results to work from. 

By making more findings available, we can help increase efficiencies and advance scientific discovery faster. 

 

To fill in the scientific record and increase reproducibility

It’s difficult to draw reliable conclusions from a set of data that we know is incomplete. This lack of information affects the entire scientific ecosystem. Readers are often unaware that negative results for a particular study may even exist, and it may even be more difficult for researchers to replicate studies where pieces of the data have been left out of the published record.

Some researchers opt to obtain specific null and negative results from outside the published literature, from non peer-reviewed depositories, or by requesting data directly from the authors. The inclusions of this “grey literature” can improve accuracy, but the additional time and effort that goes into obtaining and verifying this information would be prohibitive for many to include.

This is where publishers can play a pivotal role in ensuring that authors not only feel welcome to submit and publish negative results, but to make sure those efforts are properly recognized and credited. Published, peer-reviewed results allow for a more complete analysis of all available data and increased trust in the scientific record.  

 

We know it’s difficult to get into the lab right now and many researchers are having to rethink the way that they work or focus on other projects. We encourage anyone with previously unpublished negative and null results to submit their work to PLOS ONE and help fill in the gaps of the scientific record, or consider doing so in the future. 

 

 

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Meet the PLOS ONE Cancer and Oncology Authors

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Today is World Cancer Day — a day for raising the voices of cancer survivors, loved ones, and the people who are working endlessly to find solutions. This year’s theme is “I am and I will:” a recognition of the power each individual has to make an impact.

Each year, PLOS ONE publishes more than 1000 new research articles in cancer and oncology from authors who have dedicated their careers to studying this disease. In celebration of this years’ theme, we’re sharing their stories which inspired the science we use to understand and fight this disease. 

 

Meet the researchers…

“My research group is mainly focused on the study of lung and pancreatic cancers, which are associated with high morbidity and mortality rates, worldwide. We use high throughput methods to identify new biomarkers and regulatory pathways and functional assays to improve our understanding of disease biology. 

Our ultimate goal is to improve patient survival, through better diagnosis, prognosis and treatment.”

— Patricia Pintor dos Reis, Faculty of Medicine, São Paulo State University – UNESP Botucatu, SP, BRAZIL.

MicroRNA modulated networks of adaptive and innate immune response in pancreatic ductal adenocarcinoma. Tainara F. Felix, Rainer M. Lopez Lapa, Márcio de Carvalho, Natália Bertoni, Tomas Tokar, Rogério A. Oliveira, et al

 

“Bioinformatics is my tool and cancer research is my subject. My dad and many other people died of cancer and I want to uncover what causes cancer. And I love math and computers, which attracted me to become a bioinformatician. Now I am working for NCI initiative Ras program at Frederick National Lab for Cancer Research, which tries to tackle the most critical and ancient gene in cancer biology: Ras genes.

My last paper on PLOS ONE is about common pitfalls often seen in the survival analysis in the field. We wish to first alert researchers about the pitfalls when they perform survival analysis and to provided a novel method that shall help avoid the pitfalls.

The curiosity in biology and the desire to make life better drives my career in science.”

 

— Ming Yi, NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States of America

GradientScanSurv—An exhaustive association test method for gene expression data with censored survival outcome. Ming Yi, Ruoqing Zhu, Robert M. Stephens

 

 

“The goal of my research is to develop an agent that promotes apoptosis in cancer cells but not in normal cells. To accomplish this goal, I explored different protein targets and pathways that included but are not limited to matrix type-I metalloprotease I (MT1-MMP), tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), and oxidative stress. 

I believe that the results and proposed future strategies will help to design potent and safe cancer treatments.”

— Dmitri Rozanov, Department of Molecular and Medical Genetics, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America

Targeting mitochondria in cancer therapy could provide a basis for the selective anti-cancer activity. Dmitri Rozanov, Anton Cheltsov, Aaron Nilsen, Christopher Boniface, Isaac Forquer, et al

 

 

“I focus on H&N/Skull base cancers and mechanisms of treatment resistance within HPV positive and negative cancers.  Understanding mechanism of treatment resistance will enable us to target new pathways for improving patient outcomes.   

It is a privilege to work with folks and help the individual patient, but just as important is work on research that can possibly help the many.”

— Dukagjin Blakaj, The James Cancer Center, Ohio State University, Columbus, OH, United States of America

Association of an intact E2 gene with higher HPV viral load, higher viral oncogene expression, and improved clinical outcome in HPV16 positive head and neck squamous cell carcinoma. Nicole V. Anayannis, Nicolas F. Schlecht, Miriam Ben-Dayan, Richard V. Smith, Thomas J. Belbin, et al

 

 

“My particular area of research is the staging of colon cancer, it is important because colon cancer is a top 3 killer (of all cancer types) and we need new treatment strategies. However without accurate staging (i.e. determining how advanced the tumor is), it is nearly impossible to develop these new strategies. 

My goal is to increase this accuracy, or at least shed light on how accurate our current staging is.”

— Elias Nerad, The Netherlands Cancer Institute, Amsterdam The Netherlands.

The Apparent Diffusion Coefficient (ADC) is a useful biomarker in predicting metastatic colon cancer using the ADC-value of the primary tumor. Elias Nerad, Andrea Delli Pizzi, Doenja M. J. Lambregts, Monique Maas, Sharan Wadhwani, et al

 

 

“I have always wanted to understand the incredible organization of brain functions and how to cure patients with brain lesions. My research field focuses on brain anatomy, brain functions, neuroimaging and how all these aspects together can improve the treatment of patients with cerebral tumors. My work tried to change the standard topographical classification of brain tumors to a model including more detailed information regarding the tumor infiltration along the white matter fibers.

This model perfectly fits the open access principle because it is not based on expensive technology, rather on a basic idea merging anatomy neuroimaging and oncology. I believe that anyone in the world can reproduce this classification method with standard MRI pictures contributing to a more extensive and shared knowledge in this field.

I want to fully understand the interaction between brain structures and brain tumors to better cure my patients.”

— Francesco Latini, Department of Neuroscience, Neurosurgery, Uppsala University, Uppsala, Sweden

A novel radiological classification system for cerebral gliomas: The Brain-Grid. Francesco Latini, Markus Fahlström, Shala G. Berntsson, Elna-Marie Larsson, Anja Smits, Mats Ryttlefors

 

Read More Cancer Research on PLOS ONE

Find out more about the causes of cancer and interventions to prevent and manage the disease in the PLOS Cancer Research Special Collection.

PLOS ONE will also be launching a Call for Papers for Cancer Metastasis research and invites submissions that report on the biochemical and cell biological basis of metastasis, including but not limited to cell adhesion, cell migration, cytoskeletal dynamics, cell polarity, tumour heterogeneity, tumour dormancy and the tumour microenvironment.

 

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After the whirlwind

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Now the dust has settled after Open Access Day 2008, it’s time to bask briefly in the warm glow of what we achieved and to think about what we can improve next time.

The best way to sum up the positive feedback that we’ve received about the day is through this simple fact. We asked the 120 organizations who signed up to participate in the day, who originated from more than 27 countries, whether they would participate again next year – 90% said YES.

Then we (the organizers of Open Access Day: PLoS, SPARC and Students for Free Culture) asked ourselves whether we felt that we’d achieved our goal which was:

“To broaden awareness and understanding of Open Access, including recent mandates and emerging policies, within the international higher education community and the general public.”

Our answer was also a resounding YES. Although next year we’ll encourage participants to organize their activities at any point during “Open Access Week” to ease scheduling headaches, we’ll bring some more international folks into our organizational team, we’re seeking a technology partner, and we’ll give greater advanced notice of the next event!

We are pleased to announce that next year’s Open Access Week will be in October 2009, dates to be confirmed. To hear about the latest development please complete this form.

There were many different ways to measure the success of the 2008 day apart from the level of participation. Here are just a few of them:

• An explosion of new open access materials and their organization – not only did we create many new resources for the day but the good folks at the Open Access Directory compiled a Wiki to help organize much of the world’s material into an easy-to-use source.

• Significant blog coverage – ranging from about 400 posts about the day and the activities to over 40 superb posts in response to the synchronous blogging competition – the two winners were Dorothea Salo for her post My Father The Anthroplogist and Greg Laden for his Poem for Open Access Day.

• New Association launched – we were delighted that the Open Access Scholarly Publishers Association chose that day to announce their formation.

• New video content – we prepared six 1- minute videos presentations from a Teacher, Librarian, Funder, Student, Physician Scientist and a Patient Advocate on why Open Access Matters to them (also available on YouTube and Internet Archive), several video shout-outs (messages of support from the community) and two webcasts from Sir Richard Roberts and Dr Phil Bourne.

• Comments that we received from participants after the event –

“The day showed that we are not alone in doing OA”
“The downloadables were great, particularly “A very brief introduction to Open Access”
“It was good to let the people know the phrase – Open Access”

We’d like to make next years’ event in October 2009 bigger and better than ever. To hear about the latest developments, please complete this form.

Drum roll please – and the winner of the blogging competition is…?

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True confession. There were so many entires of such a high standard that in the end the judges decided to have 2 winners. I am going to cross post both in full to the plos.org blog site in a few minutes. They are:

Dorothea Salo, for her post My Father The Anthropologist. The judges comments about this post were:

  • “Very personal, very well-written, just as we wanted!” Bora, Scientist and Blogger, A Blog Around the Clock.
  • “Warm and engaging, I thoroughly enjoyed this.” Liz, PLoS Communications.

On hearing of her joint win Dorothea said “you made my day.”

Dorothea Salo’s professional interests include scholarly communication, usability and design, data curation, and digital preservation. She is the Digital Repository Librarian at the University of Wisconsin, where she serves the state university system’s consortial institutional repository, MINDS@UW.

Greg Laden who wrote A poem for Open Access Day. The judges comments about this post were:

  • “Epic success! A winner. Brilliant.” Aaron, Scientist and Blogger, Wired Science.
  • “Funny and uses one of my favorite phrases “democratization of information” superb.” Liz, PLoS Communications.

On hearing of his joint in Greg said “Wow, this is the FIRST TIME I’ve ever won anything! Thank you!. Well, the first time in a while, anyway”. He then blogged the news for your enjoyment.

Greg Laden is part time independent scholar and part time adviser with the Program for Individualized Learning, University of Minnesota. He is also on one or more graduate faculties at The U, depending on the status of various graduate students. He has a PhD in Archeology and Biological Anthropology, and is interested in human evolution; the biology of gender and sexuality; and the biology of race. He conducts field research in Africa. His most recent paper, with Gil Tostevin and Mischa Pen, is an evaluation of a traveling exhibit on race and racism, and is published in the journal Museum Anthropology.

Warmest Congratulations to both our winners and thanks to everyone who entered. We will be sending them each a bag of swag in the next few days.