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\begin{document}

\title{Interactive and discoverable preprints\\}


 \author{The Authorea Team}


\date{}

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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,
\emph{how we communicate them is important.}\\

\subsection*{Write, edit, make public as
preprints}\label{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 \emph{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~\href{https://www.authorea.com/signup}{join us!}~\\\selectlanguage{english}
\begin{figure}[h!]
\begin{center}
\includegraphics[width=1.00\columnwidth]{figures/Screen-Shot-2016-08-18-at-8.23.47-AM/Screen-Shot-2016-08-18-at-8.23.47-AM}
\caption{{\hypertarget{auto-label-caption-614077}{}
Readers~prefer typeset documents in HTML with access to references and
databases via hyperlinks. Source:
\href{http://asapbio.org/wp-content/uploads/2016/05/Preprint-server-preferences-survey.pdf}{Preferences
in Preprints}%
}}
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\subsection*{}\label{section}

\subsection*{What are researchers writing on
Authorea}\label{what-are-researchers-writing-on-authorea}

\textbf{}\\

\textbf{Ebola~virus epidemiology, transmission, and evolution during
seven months in Sierra Leone} (\cite{Park_2015}~et al., \emph{Cell})\\

\begin{quote}
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.
\href{https://www.authorea.com/users/10734/articles/19957/_show_article}{{[}Read
More{]}}\\
\end{quote}

\textbf{The Microbes We Eat} (\selectlanguage{english}\cite{Lang_2014}, \emph{PeerJ})\\

\begin{quote}
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~{6X1066X106}and~{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
-~\emph{i.e.}, ingested as foods - are important contributors to the
composition, inter-individual variation, and function of our gut
microbiota.~\href{https://www.authorea.com/users/5064/articles/5319/_show_article}{{[}Read
More{]}}\\
\end{quote}

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