The power of the atomAt the beginning of the 20th century, major advancements in our understanding of fundamental physics led scientists to the discovery of nuclear energy. An unprecedented amount of power could in principle be released by combining (nuclear fusion) or breaking (nuclear fission) certain atomic species under special conditions. Nuclear fusion in particular was understood to be the process powering the immense luminosity of stars, including our Sun. Nuclear fusion is the energy source illuminating our Universe.Why so much energy?Burning fossil fuels releases chemical energy. This chemical energy is stored in the mild electromagnetic interactions between atoms in a compound. Nuclear energy, on the other hand, comes from the very central regions of the atom.  As the name suggests, it is stored in the nuclei, which are kept together by the strong force. The strong force is much stronger than all the other forces, including the electromagnetic one. As a result, nuclear fuel has an energy density about ten million times larger than chemical fuel. If your car was running on nuclear fuel, its gas mileage would be something like hundreds of millions of MPG. From light to darknessThe physics revolution that characterized the first three decades of the 20th century and led to the development of quantum mechanics and nuclear physics, was followed by the second World War. In 1942, the United States started a very ambitious project to build a nuclear weapon. The Manhattan Project, led by Robert Oppenheimer and gathering some of the best physicists on the planet, culminated with the successful Trinity experiment in 1945 (Fig.\ref{982837}). The first detonation of a nuclear weapon was the most shocking demonstration of the great power of science and the scientific method. Only less than a month later, two nuclear bombs were dropped over the Japanese cities of Hiroshima and Nagasaki, resulting in the end of WWII and the death of hundreds of thousands of people. The sheer destruction inflicted by the atomic bomb left an indelible mark on humankind's consciousness, formally starting a new era in the history of man. An era of greater responsibility. While no nuclear weapons have been purposely used in war ever since, more than 2000 nuclear tests have been performed after the Trinity, Hiroshima and Nagasaki explosions.  

This example manuscript is intended to serve as a tutorial and template for authors to use when writing their own AAS Journal articles with Authorea. The manuscript includes a history of   and documents the new features in the previous version, 6.0, as well as the new features in version 6.1. This manuscript includes figure and table examples to illustrate these new features. AUTHOREA FEATURES A RICH TEXT EDITOR SO THAT YOU CAN WRITE IN LATEX, MARKDOWN, OR RICH TEXT AND RENDER DIRECTLY ON THE WEB. AUTHOREA SUPPORTS AND RENDERS THE VAST MAJORITY OF LATEX NOTATION NEEDED FOR AAS JOURNAL ARTICLES. A FEW FEATURES PROVIDED BY AASTEX V6.1. THAT ARE NOT AVAILABLE IN AUTHOREA HAVE BEEN LISTED IN THIS DOCUMENT. Authors are welcome replace the text, tables, figures, and bibliography with their own and submit the resulting manuscript to the AAS Journals peer review system. The first lesson in the tutorial is to remind authors that the AAS Journals, the Astrophysical Journal (ApJ), the Astrophysical Journal Letters (ApJL), and Astronomical Journal (AJ), all have a 250 word limit for the abstract. If you exceed this length the Editorial office will ask you to shorten it.

This example manuscript is intended to serve as a tutorial and template for authors to use when writing their own AAS Journal articles. The manuscript includes a history of   and documents the new features in the previous version, 6.0, as well as the new features in version 6.1. This manuscript includes many figure and table examples to illustrate these new features. Information on features not explicitly mentioned in the article can be viewed in the manuscript comments or more extensive online documentation. Authors are welcome replace the text, tables, figures, and bibliography with their own and submit the resulting manuscript to the AAS Journals peer review system. The first lesson in the tutorial is to remind authors that the AAS Journals, the Astrophysical Journal (ApJ), the Astrophysical Journal Letters (ApJL), and Astronomical Journal (AJ), all have a 250 word limit for the abstract. If you exceed this length the Editorial office will ask you to shorten it.

The arXiv is the most popular preprint repository in the world. Since its inception in 1991, the arXiv has allowed researchers to freely share publication-ready articles prior to formal peer review. The growth and the popularity of the arXiv emerged as a result of new technologies that made document creation and dissemination easy, and cultural practices that incentivized collaboration and data sharing. The arXiv represents a unique place in the history of research communication and the Web itself, however it has arguably changed very little since its creation.  Here we look at the strengths and weaknesses of arXiv in an effort to identify what possible improvements can be made based on new technologies not previously available. Based on this, we argue that a modern arXiv might in fact not look at all like the arXiv of today.  

INTRODUCTION Lorem ipsum dolor sit amet, consectetur adipiscing elit. Cras egestas auctor molestie. In hac habitasse platea dictumst. Duis turpis tellus, scelerisque sit amet lectus ut, ultricies cursus enim. Integer fringilla a elit at fringilla. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla congue consequat consectetur. Duis ac mi ultricies, mollis ipsum nec, porta est. Mauris nec massa leo. Mauris ac diam auctor nisl imperdiet porta. Sed sit amet neque eget nisi dictum placerat. Duis sit amet pellentesque odio. Cras scelerisque sem a consectetur vehicula. Aliquam interdum luctus fringilla. Nunc sollicitudin, lorem in semper viverra, dui nisi sodales sem, ut condimentum erat leo eget arcu. Donec pharetra aliquam metus, non pulvinar tellus interdum a. Mauris a ante pharetra, mollis enim in, eleifend erat. Pellentesque suscipit risus massa, non vestibulum libero euismod feugiat. In hac habitasse platea dictumst. Maecenas rutrum lobortis lobortis. Vestibulum convallis porttitor sem ac ultricies. Mauris volutpat fringilla nisl blandit semper. Proin nec iaculis sem. Aenean neque ipsum, pretium a faucibus non, tincidunt ut sapien. Nunc a aliquet sem, eget aliquet purus. Vestibulum ac placerat mauris. Proin sed dolor ac justo semper iaculis. Donec varius, nibh sit amet finibus tristique, sapien ante interdum odio, et pretium sapien libero nec massa. In hac habitasse platea dictumst. Donec vel augue ac sapien imperdiet pretium. Maecenas gravida risus id ultricies dignissim. Maecenas gravida felis quis dolor faucibus, sed maximus lorem tristique. Nam hendrerit quam quis ante porta posuere. Fusce finibus maximus orci at porttitor. Nulla tempor ex a porttitor consequat. Quisque quis tempor eros. Donec nisi mauris, sollicitudin in dapibus eu, interdum ultricies quam. Pellentesque tincidunt lobortis orci non venenatis. Cras in justo luctus, pulvinar augue id, suscipit diam. Morbi aliquet fringilla nibh, vel pellentesque dui venenatis eget. Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus. Donec ultricies ultrices magna gravida porta. Maecenas accumsan diam dui, auctor ornare ex pellentesque id. Integer tempus massa id augue finibus convallis. Nulla vestibulum, nisl id tempor pulvinar, felis dui pellentesque lacus, quis bibendum metus enim sed ex. Duis magna nunc, rutrum sodales elementum a, egestas eget dolor. Vivamus non pretium nunc, at vestibulum arcu. Vivamus pharetra, justo vel blandit feugiat, magna neque feugiat mi, a bibendum erat arcu a est. Sed vestibulum, leo non elementum condimentum, dui ipsum vehicula quam, a vehicula turpis ipsum a nibh. Mauris posuere lobortis porta. Aenean augue neque, varius vitae dapibus ac, dictum ut nisl.

These instructions give you guidelines for preparing papers for IEEE TRANSACTIONS and JOURNALS. Use this document as a template if you are using Microsoft Word 6.0 or later. Otherwise, use this document as an instruction set. The electronic file of your paper will be formatted further at IEEE. Define all symbols used in the abstract. Do not cite references in the abstract. Do not delete the blank line immediately above the abstract; it sets the footnote at the bottom of this column.

AbstractPreprints are widely acknowledged to be beneficial to the research community. However, the career implications of an author preprinting their work are unclear. Here we discuss the implications of researchers preprinting their work in terms of precedence, visibility and citation impact, and manuscript editing. In short, we show that researchers that preprint their work have a citation boost ranging from 83% to 269% and that preprints can in practice improve your manuscript and that can limit "scooping."What are preprints?Preprints are publication-ready research articles that have yet to undergo peer review and be formally published. They are free, openly accessible, and widely reusable under permissive copyright licenses.  They accelerate research communication by putting dissemination under researcher control. While preprints are widely viewed as beneficial for research and are the norm in certain disciplines like physics, math, computer science, and statistics, preprinting is relatively new in other disciplines, like the life sciences, psychology, sociology and others.  In these fields - that are new to preprints - questions and confusion can arise around preprinting, potentially hampering their uptake and utility.The benefits of preprintingBelow we highlight the benefits of preprinting your work at the individual level in an effort to encourage researchers to take control of their research. This article aims to show that preprinting is not just good for the community, but also good for the individual scientist, as outlined in "The selfish scientist’s guide to preprint posting" \cite{Kriegeskorte}.Preprints allow researchers to claim precedence on a discoveryWith funding rates at an all-time historic low (see figure \ref{849950}) researchers are hyper-competitive in many aspects of their careers. This competition, while good to an extent, can severely limit data sharing and open discussion, two practices necessary for the advancement of research.  One particular fear of researchers is that they might be "scooped," (ie their discovery is shared by someone else first).  

What is the ArXiv?The arXiv, or actually, ar\(\chi\)iv (pronounced "archive", since \(\chi\) = "chi" 🤓 ) is the most popular preprint repository in the world. (Read: What is a preprint?) It was started in 1991 by physicist Paul Ginsparg (hi Paul! 👋 ) to become a way to quickly and freely give the scientific community access to the submission-ready research papers, as e-prints. While the arXiv initially covered only the fields of physics and astronomy, it grew over time to encompass other fields, such as computer science, quantitative biology, statistics, and quantitative finance. The rise of arXiv has been mostly limited to fields that use LaTeX, a typesetting system for math-heavy documents. This is because:  (1) the most efficient way to submit papers to arXiv is by uploading a LaTeX file which gets compiled to PDF, and (2) pre-printing has historically been a practice popular in the hard sciences --- at CERN, it was performed via inter-library exchange of scanned papers before the web even existed \cite{pepe2005cern}. However, in recent years, pre-prints are catching on as a free (and legal!) mechanism to openly and quickly share research also in the life sciences (see ASAPbio, and BiorXiv, for example).How do ArXiv and Authorea compare?At first glance, ArXiv and Authorea may not seem related to one another. ArXiv is a content repository, while Authorea is a content creation system. However, Authorea - with the launch of a number of publishing features - is quickly becoming an open repository, as well. We think that the open research repository of the future will have a lot of the features and traits that Authorea is developing. Here's why:1. A scholarly repository is more than a PDF dumpThere is growing consensus in scholarly communication circles that academic publishing needs to move "beyond the PDF" (see the manifesto of Force 11). PDFs are a great portable format for printing, but they are not the best format to share, discuss, and read on the web. Every article on arXiv is a PDF (built from LaTeX). As such, it is static, 2-dimensional and non-actionable. It is not a stretch to say that a paper in PDF is merely a digital photograph of a piece of paper. We can, and are doing, better than that. Authorea's repository is a collection of Open Access and Open Science (i.e. data driven) web native papers.

Preprints are publication-ready research papers that are made public before publication

What is the preprint server ArXiv?The ar\(\chi\)iv (pronounced "archive", since \(\chi\) = "chi") is the most popular preprint repository in the world. (Read: What is a preprint?) It was started in 1991 by physicist Paul Ginsparg to become a way to quickly and freely give the scientific community access to the submission-ready research papers, as e-prints. While the arXiv initially covered only the fields of physics and astronomy, it grew over time to encompass other fields, such as computer science, quantitative biology, statistics, and quantitative finance. The rise of arXiv has been mostly limited to fields that use LaTeX, a typesetting system for math-heavy documents. This is because (1) the most efficient way to submit papers to arXiv is by uploading a LaTeX file which gets compiled to PDF, and (2) pre-printing has historically been a practice popular in the hard sciences --- at CERN, it was performed via inter-library exchange of printed copies before the web even existed \cite{pepe2005cern}. However, in recent years, pre-prints are catching on as a legal and free mechanism to openly and quickly share research also in the life sciences (see ASAPbio, and BiorXiv, for example).How do ArXiv and Authorea compare?At first glance, ArXiv and Authorea may not seem related to one another. ArXiv is a content repository, while Authorea is a content creation system. However, Authorea - with the launch of a number of publishing features - is quickly becoming an open repository, as well. Below, we highlight some points of comparison between Authorea and ArXiv.1. More than just a collection of PDFs: web native papers.There is growing consensus in scholarly communication circles that academic publishing needs to move "beyond the PDF" (see Force 11 conference). The PDF is a great portable format for printing, but it is not the best format to share, discuss, and read on the web. Every article on arXiv, being a PDF, is non-actionable. In this respect, the arXiv is a "PDF dump".2. For LaTeX users. And for everyone else too!The ArXiv relies heavily on LaTeX. For Authorea, LaTeX is one of many  formats you can write in. Others include Markdown, and HTML (rich text, like Word!). Authorea offers a format-neutral, web-native platform. Regardless of the format, you render content on the web - not on a separate pane that compiles a PDF (side note, you can still export a PDF). The advantage: Authorea documents are not constrained to the hard sciences and to the LaTeX community. Authorea is for all scholars: from astrophysics to zoology. Authorea's rich text editor is a true WYSIWYG editor (What you see is what you get). It also has the ability to include as much LaTeX and mathematical notation as you need. Every document written in Authorea becomes a beautiful webpage.

In this document, you can find a number of examples showing how to typeset beautiful mathematical equations with LaTeX. In the first part of the document, you find the examples. At the bottom, in section \ref{sec:source}, you find the full code to generate these examples. A more generic guide on how to insert LaTeX blocks in your documents can be found here.

I seek to explore various frequentist and Bayesian methods for drawing conclusions about genetics of gene regulation, both for cis- and trans- association studies, in the context of RNA-seq dataset with known/inferred confounders.IntroductionIn their paper Bayesian new statistics: https://link.springer.com/article/10.3758/s13423-016-1221-4, Kruschke and Liddell explain the divide in the statistical community, between frequentist and Bayesian methods, and between estimation and quantification of uncertainty. Not only do the authors recommend a shift from the former to the latter in both respects, they also try to point out that additional aspects of statistical analyses such as meta-analysis, randomized controlled trials and power analysis may benefit from this shift.Being aware of this recommendation, and also of the recent advances in deep sequencing projects that provide rich information about variation in genotypes, expression and other phenotypes of interest in a variety of settings, I would like not only review, but also further develop, methods that seek to reason about this transition in genomics. As a first step, I focus on RNA-seq studies with genotyping information, which provide a proxy to overall expression levels of proteins and thus cellular activity in a system of interest, and also the potential to separate out genetic and non-genetic basis of variation in expression, giving us important insights into regulatory mechanisms of these systems.Primer: RNA-seq workflow, problems and (partial) solutionsIn this primer, I go through our current (and some not yet implemented) RNA-seq workflow, organizing them into problems and (partial) solutions. In cases where the solution is insufficient (which is true in most cases), I've marked them as possible paper topics.dbGaP - https://www.ncbi.nlm.nih.gov/gapSRA library - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=run_browserFirst, we can take the sequence library form an experiment, usually in *.fastq format, from public studies shared in the above resources, or from a proprietary dataset. We are currently working with Illumina 76-bp paired-end RNA-seq reads in the case of GTEx data, but certainly are not limited to this setup.Problem:We need to make sure the that the reads are not contaminated (adapter sequences, other non-human reads, etc.), have no unexpected biases, and that the reads have sufficient quality score. In addition, usually the sequences towards the end have poor read quality, and we want to be able to account for this.A solution:Use FastQC and Trimmomatic to perform QC and trim reads for poor quality ends:FastQC manual: https://biof-edu.colorado.edu/videos/dowell-short-read-class/day-4/fastqc-manualTrimmomatic manual: http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdfOptional: An example FastQC output from a real GTEx sample:

At Authorea we have big goals, not necessarily for ourselves, but for researchers and the scientific community. We envision a world where researchers write and publish their work openly, they include their data inside of interactive figures and seek collaborators and the community to test their work to ensure it is robust. Communication and publishing is dynamic and modern and research moves more efficiently because researchers move more efficiently. This vision may sound idealistic but it is being realized and we are diligently working to build a platform and community to foster it.  Over the last year we have taken tremendous steps towards creating the place to write and disseminate research. We relaunched our new editor only a few months ago and have redesigned nearly every part of Authorea to make it the best place to write research documents, for all researchers.  We've added direct submission to a growing list of leading journals, have introduced the first and only place to preprint in HTML, and introduced a new version control system for writing research papers.  In short, we've done a lot, really fast.We're going to continue to keep innovating but we're taking a brief pause from introducing new features to focus on reliability, usability, and research support. That means, we want to hear from you. What could we do better? What small or big changes on Authorea would help you be more efficient at research writing and publishing? Below are just some of the major highlights of what we've accomplished in the last few months, which do not include the bugs here and there and tweaks made based on user feedback/testing.  Acquire Research Publisher, The Winnower--LinkNew HomepageLaunch Authorea Beta, our new editor--Linkreal-time collaborationautosaveability to write in Markdown, LaTeX, and rich-text all within one articlenew toolbarPartner with Sample of Science--LinkPartner with eLife for direct submission--LinkImproved UX for LaTeX and Markdown rendering.Improved Author Management controlAdd multi-cite capability/improve design UX of citation tool.New pricing--LinkNew browse page--LinkIntroduce new version control system for research writing--LinkNew features page--LinkIntroduce preprinting capabilities and ability to issue DOI on Authorea--LinkAdd \labels, \refs, New commenting system

Today's research is truly awesome. Researchers can now analyze and perform experiments that would have been thought impossible only a few decades ago. From the deep sequencing of nearly any animal genome with ease \cite{DePristo_2011} to the discovery of the Higgs Boson \cite{ATLAS_Collaboration_2012}, we are in a period of great innovation and understanding.  And yet, how we share our ideas (i.e. publishing) has not changed very much in nearly 350 years.  In short, scientists are doing 21st-century research, writing on 20th-century tools, and packaging it in 17th-century formats.The fact that research communication hasn't changed in hundreds of years may signal that it works, right? Well in some regards--yes, the work is persistent and we have copies of some of the world's most important ideas (yay librarians!). Yet, in many other regards research communication is failing us: data sharing is rare \cite{Alsheikh_Ali_2011}, the majority of work is hard to access (it's pay-walled) \cite{Bj_rk_2010}, publishing takes months to years to complete \cite{Himmelstein_2016}, and classical peer review does not detect major errors \cite{Smith_2010}. As a consequence, we're now seeing major problems with the reproducibility of findings in disciplines like cancer research and psychology \cite{Begley_2012,eLife_2017,Open_Science_Collaboration_2015}.To understand how we got to where we are today, it is useful to look at the history of research publishing, how and why it got started, and the changes that occured along the way. Here, we outline an very brief history of research publishing, with particular emphasis on preprints, in hopes of providing a stage to discuss what publishing might look like in the near future.A brief history of the research journalThe first journal article, published in 1655, by Philosophical Transactions marked a step towards the formalization of the communication of research in article format \cite{Oldenburg_1665}. As noted in the introductory editorial, research communication was seen as necessary for the advancement of research: "Whereas there is nothing more necessary for promoting the improvement of Philosophical Matters, than the communication of such" \cite{1665}.

Since 1988, according to Scopus, there have been 48,238,173 documents published by an estimated 100M+ authors.  Most of these papers are written by lifelong academics and professional researchers -- however, occasionally somebody who spends more of their time in the public eye than in the lab makes a splash and publishes a piece of original research. In this post we highlight 10 publications with nontraditional authors.1. Bringing Impressionism to Life with Neural Style Transfer in Come SwimAuthor: Kristen Stewart (Actress).Citation: \cite{Josh_2017}.Citation count: 0

Authorea is on a mission to build the best research document editor and publishing platform ever made. We believe that the best way to accelerate scientific discovery is to give full control of document creation and distribution to the researcher, and that the best way to do that is to build a web-based editor that enables researchers to collaborate and disseminate their work seamlessly.Authorea,  like many research projects, started with a question: Why is the research writing process so slow? We started with the rough notion that the internet age was failing to deliver optimal tools for things like collaborative writing and submitting works to publishers.  We refined this core idea and launched Authorea two years ago.Since then, we've devoted tens of thousands of hours to understand how to build software that makes it easier for researchers to do groundbreaking work. At the beginning of this year, we started building our new editor -- Authorea Beta -- the editor that will bring Authorea to the mainstream to benefit researchers in every discipline.Today, we're happy to share with you Authorea Beta. Writing research online has tremendous potential for collaboration, dissemination, and discovery. We're here to bring writing online to researchers and we'll be with you every step. 

"Like every great river and every great sea, the moon belongs to none and belongs to all. It still holds the key to madness, still controls the tides that lap on shores everywhere, still guards the lovers who kiss in every land under no banner but the sky". E.B. White The New Yorker, July 26, 1969Where does the Moon come from?Scientist believe that our Moon formed out of a ‘giant impact’ that occurred between a Mars-sized planet and the early Earth, some 4.5 billion years ago. The Moon was then formed from the coalescence of the orbiting debris scattered during the impact.Recent results seem to confirm this scenario

Stellar ultrasounds. Certain stars pulsate and can effectively be considered huge musical instruments: depending on their size and internal structure, they can oscillate at different frequencies, somewhat similar to spherical drums of different size, shape and material. The waves that propagate through the star can bring to surface precious information about the internal regions they crossed. This is similar to what seismologists do with the planet: they study at the surface waves excited by earthquakes to retrieve information about the structure and properties of the Earth’s inner regions they crossed. The waves crossing a star can be of different types, some are similar to sound waves, others to surf waves. Different waves probe different regions of the stellar plasma, so depending on which type of waves astronomers 'listen to', they can retrieve properties relative to different stellar depth. This is the basic idea behind the 'stellar ultrasound'. It turns out that the oscillations induced by these different types of waves can be encoded directly in the light of the star. This is awesome, because the sound can not travel in the vacuum that is the medium between stars, but light can. Also it travels much faster. This opens up a new branch of astronomy called "Asteroseismology", something only recently we started applying to large collections of stars because it requires observations from space. We can now determine the internal properties of thousands of stars. Some of these stars are thousands of light years away! And we found many surprises. The latest discovery is the potential ubiquity of ultra-strong magnetic fields hiding in the stellar cores. The stellar core is the region where thermonuclear reactions are at play, making the star shine and basically creating all the elements of which humans are made off as a byproduct (except Hydrogen). These magnetic fields are million of times stronger than the Earth's magnetic field, and can change completely the way a star lives and dies! For example, they might be playing a role in producing the brightest explosions in the cosmos...  Stars are huge musical instruments, playing music with their starlight. This twinkling carries the secret story of their magnetic coresSource: - Science (http://science.sciencemag.org/content/350/6259/423.abstract), - Nature (http://www.nature.com/nature/journal/v529/n7586/full/nature16171.html)