Interactive and discoverable preprints

The Authorea Team

Scholarly communication is advancing culturally and technologically towards a better future.  There are an increasing number of disciplines and people publishing their content under open-access licenses, publishing their work as preprints, and publishing different types of content from data to posters to single figures. We're happy to be part of this push towards a more dynamic and transparent system of communication. In fact, it's one of the reasons we exist--to improve how leading researchers and student's alike communicate their ideas amongst each other and to the world. These are the world's most important ideas, how we communicate them is important.

Write, edit, make public as preprints

Authorea is predominantly used as an editor where researchers write their papers, but we're not just an editor. In fact, many researchers choose to write on Authorea because after they are done writing they are also done "preprinting." In short, Authorea is a collaborative text editor and a preprint repository. Like other preprint repositories, we allow immediate and open communication amongst researchers and the public. What sets us apart is how we do this. Each article is in itself a git repository where researchers can directly host data with their manuscripts. We are not limited by discipline or content type and we allow, even encourage, other forms of grey literature (informal documents) to be published with us, such as blogs, how-to's, class notes, abstracts, etc. Moreover, whereas all preprint repositories publish their articles in the portable document format, otherwise known as the PDF (some even host Microsoft Word files!), Authorea has reinvented how articles are written and presented and to utilize all the capabilities of the web.  

We built Authorea to usher in the future of research writing, so come join us! 




Readers prefer typeset documents in HTML with access to references and databases via hyperlinks. Source: Preferences in Preprints



What are researchers writing on Authorea


Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone (Park 2015 et al., Cell)
The 2013-2015 Ebola virus disease (EVD) epidemic is caused by the Makona variant of Ebola virus (EBOV). Early in the epidemic, genome sequencing provided insights into virus evolution and transmission, and offered important information for outbreak response. Here we analyze sequences from 232 patients sampled over 7 months in Sierra Leone, along with 86 previously released genomes from earlier in the epidemic. We confirm sustained human-to-human transmission within Sierra Leone and find no evidence for import or export of EBOV across national borders after its initial introduction. Using high-depth replicate sequencing, we observe both host-to-host transmission and recurrent emergence of intrahost genetic variants. We trace the increasing impact of purifying selection in suppressing the accumulation of nonsynonymous mutations over time. Finally, we note changes in the mucin-like domain of EBOV glycoprotein that merit further investigation. These findings clarify the movement of EBOV within the region and describe viral evolution during prolonged human-to-human transmission. [Read More]

The Microbes We Eat (Lang 2014, PeerJ)
Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: 1) the Average American (AMERICAN): focused on convenience foods, 2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and 3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3X1091.3X109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6X1066X106and 1.4X1061.4X106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbial approaches beyond probiotics taken as supplements - i.e., ingested as foods - are important contributors to the composition, inter-individual variation, and function of our gut microbiota. [Read More]

References

  1. Daniel J. Park, Gytis Dudas, Shirlee Wohl, Augustine Goba, Shannon L.M. Whitmer, Kristian G. Andersen, Rachel S. Sealfon, Jason T. Ladner, Jeffrey R. Kugelman, Christian B. Matranga, Sarah M. Winnicki, James Qu, Stephen K. Gire, Adrianne Gladden-Young, Simbirie Jalloh, Dolo Nosamiefan, Nathan L. Yozwiak, Lina M. Moses, Pan-Pan Jiang, Aaron E. Lin, Stephen F. Schaffner, Brian Bird, Jonathan Towner, Mambu Mamoh, Michael Gbakie, Lansana Kanneh, David Kargbo, James L.B. Massally, Fatima K. Kamara, Edwin Konuwa, Josephine Sellu, Abdul A. Jalloh, Ibrahim Mustapha, Momoh Foday, Mohamed Yillah, Bobbie R. Erickson, Tara Sealy, Dianna Blau, Christopher Paddock, Aaron Brault, Brian Amman, Jane Basile, Scott Bearden, Jessica Belser, Eric Bergeron, Shelley Campbell, Ayan Chakrabarti, Kimberly Dodd, Mike Flint, Aridth Gibbons, Christin Goodman, John Klena, Laura McMullan, Laura Morgan, Brandy Russell, Johanna Salzer, Angela Sanchez, David Wang, Irwin Jungreis, Christopher Tomkins-Tinch, Andrey Kislyuk, Michael F. Lin, Sinead Chapman, Bronwyn MacInnis, Ashley Matthews, James Bochicchio, Lisa E. Hensley, Jens H. Kuhn, Chad Nusbaum, John S. Schieffelin, Bruce W. Birren, Marc Forget, Stuart T. Nichol, Gustavo F. Palacios, Daouda Ndiaye, Christian Happi, Sahr M. Gevao, Mohamed A. Vandi, Brima Kargbo, Edward C. Holmes, Trevor Bedford, Andreas Gnirke, Ute Ströher, Andrew Rambaut, Robert F. Garry, Pardis C. Sabeti. Ebola Virus Epidemiology Transmission, and Evolution during Seven Months in Sierra Leone. Cell 161, 1516–1526 Elsevier BV, 2015. Link

  2. Jenna M. Lang, Jonathan A. Eisen, Angela M. Zivkovic. The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types. PeerJ 2, e659 PeerJ, 2014. Link

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