AUTHOREA
Log in Sign Up Browse Preprints
LOG IN SIGN UP

Preprints

Explore 46,419 preprints on the Authorea Preprint Repository

A preprint on Authorea can be a complete scientific manuscript submitted to a journal, an essay, a whitepaper, or a blog post. Preprints on Authorea can contain datasets, code, figures, interactive visualizations and computational notebooks.
Read more about preprints.

Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts...
Charles Pepe-Ranney
Chantal Koechli

Charles Pepe-Ranney

and 3 more

May 30, 2014
ABSTRACT Biological soil crusts (BSC) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface. In particular, BSC N₂-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems. In mature crusts, N₂-fixation is largely attributed to heterocystous cyanobacteria, however, early successional crusts possess few N₂-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N₂-fixation during the critical early stages of BSC development. DNA stable isotope probing (DNA-SIP) with ¹⁵N₂ revealed that _Clostridiaceae_ and _Proteobacteria_ are the most common microorganisms that assimilate ¹⁵N₂ in early successional crusts. The _Clostridiaceae_ identified are divergent from previously characterized isolates, though N₂-fixation has previously been observed in this family. The Proteobacteria identified share >98.5 %SSU rRNA gene sequence identity with isolates from genera known to possess diazotrophs (e.g. _Pseudomonas_, _Klebsiella_, _Shigella_, and _Ideonella_). The low abundance of these heterotrophic diazotrophs in BSC may explain why they have not been characterized previously. Diazotrophs play a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSC in arid ecosystems. KEYWORDS: microbial ecology / stable isotope probing / nitrogen fixation / biological soil crusts
Ternary Ladder Operators
Benedict Irwin

Benedict Irwin

November 02, 2020
ABSTRACT We develop a triplet operator system which encompasses the structure of quark combinations. Ladder operators are created. The constants β are currently being found.
Counting the Cost: A Report on APC-supported Open Access Publishing in a Research Lib...
Mark Newton
Eva T. Cunningham

Mark Newton

and 2 more

May 12, 2014
At one-hundred twenty-two articles published, the open access journal _Tremor and other Hyperkinetic Movements_ (tremorjournal.org, ISSN: 2160-8288), is growing its readership and expanding its influence among patients, clinicians, researchers, and the general public interested in issues of non-Parkinsonian tremor disorders. Among the characteristics that set the journal apart from similar publications, _Tremor_ is published in partnership with the library-based publications program at Columbia University’s Center for Digital Research and Scholarship (CDRS). The production of _Tremor_ in conjunction with its editor, a researching faculty member, clinician, and epidemiologist at the Columbia University Medical Center, has pioneered several new workflows at CDRS: article-charge processing, coordination of vendor services, integration into PubMed Central, administration of publication scholarships granted through a patient-advocacy organization, and open source platform development among them. Open access publishing ventures in libraries often strive for lean operations by attempting to capitalize on the scholarly impact available through the use of templated and turnkey publication systems. For CDRS, production on _Tremor_ has provided opportunity to build operational capacity for more involved publication needs. The following report introduces a framework and account of the costs of producing such a publication as a guide to library and other non-traditional publishing operations interested in gauging the necessary investments. Following a review of the literature published to date on the costs of open access publishing and of the practice of journal publishing in academic libraries, the authors present a brief history of the _Tremor_ and a tabulation of the costs and expenditure of effort by library staff in production. Although producing _Tremor_ has been more expensive than other partner publications in the center's portfolio, the experiences have improved the library's capacity for addressing more challenging projects, and developments for _Tremor_ have already begun to be applied to other journals.
Large-Scale Automated Proactive Road Safety Analysis Using Video Data
Paul St-Aubin
Nicolas Saunier

Paul St-Aubin

and 2 more

May 06, 2014
Due to the complexity and pervasiveness of transportation in daily life, the use and combination of larger data sets and data streams promises smarter roads and a better understanding of our transportation needs and environment. For this purpose, ITS systems are steadily being rolled out, providing a wealth of information, and transitionary technologies, such as computer vision applied to low-cost surveillance or consumer cameras, are already leading the way. This paper presents, in detail, a practical framework for implementation of an automated, high-resolution, video-based traffic-analysis system, particularly geared towards researchers for behavioural studies and road safety analysis, or practitioners for traffic flow model validation. This system collects large amounts of microscopic traffic flow data from ordinary traffic using CCTV and consumer-grade video cameras and provides the tools for conducting basic traffic flow analyses as well as more advanced, pro-active safety and behaviour studies. This paper demonstrates the process step-by-step, illustrated with examples, and applies the methodology to a case study of a large and detailed study of roundabouts (nearly 80,000 motor vehicles tracked up to 30 times per second driving through a roundabout). In addition to providing a rich set of behavioural data about Time-to-Collision and gap times at nearly 40 roundabout weaving zones, some data validation is performed using the standard Measure of Tracking Accuracy with results in the 85-95% range.
Agroforestry: An adaptation measure for sub-Saharan African food systems in response...
Robert Orzanna
Nika Scher

Robert Orzanna

and 1 more

April 06, 2017
This paper examines the impact of increasing weather extremes due to climate change on African food systems. The specific focus lies on agroforestry adaptation measures that can be applied by smallholder farmers to protect their livelihoods and to make their food production more resilient against the effects of those weather extremes. The adoption potentials for agroforestry is evaluated, taking into consideration regional environmental and socio-economic differences, and possible barriers for adoption with respect to extrinsic and intrinsic factors are outlined. According to the indicators that approximate extrinsic factors, a high adoption potential for agroforestry is likely to be found in Angola, Botswana, Cameroon, Cabo Verde, Gabon, Ghana, Mauritania and Senegal. A very low potential exists in Somalia, Eritrea, South Sudan and Rwanda.
Science was always meant to be open
Alberto Pepe

Alberto Pepe

February 22, 2017
Here’s my crux: I find myself criticizing over and over the way that scientific articles look today. I have said many times that scientists today write 21th-century research, using 20th-century tools, packaged in a 17th-century format. When I give talks, I often use 400-year-old-articles to demonstrate that they look and feel similar to the articles we publish today. But the scientific article of the 1600’s looked that way for a reason. This forthcoming article by explains: In the early 1600s, Galileo Galilei turned a telescope toward Jupiter. In his log book each night, he drew to-scale schematic diagrams of Jupiter and some oddly-moving points of light near it. Galileo labeled each drawing with the date. Eventually he used his observations to conclude that the Earth orbits the Sun, just as the four Galilean moons orbit Jupiter. History shows Galileo to be much more than an astronomical hero, though. His clear and careful record keeping and publication style not only let Galileo understand the Solar System, it continues to let anyone understand how Galileo did it. Galileo’s notes directly integrated his data (drawings of Jupiter and its moons), key metadata (timing of each observation, weather, telescope properties), and text (descriptions of methods, analysis, and conclusions). Critically, when Galileo included the information from those notes in Siderius Nuncius, this integration of text, data and metadata was preserved:
Two Local Volume Dwarf Galaxies Discovered in 21 cm Emission: Pisces A and B
Erik Tollerud
Marla Geha

Erik Tollerud

and 4 more

April 15, 2014
INTRODUCTION The properties of faint dwarf galaxies at or beyond the outer reaches of the Local Group (1 − 5 Mpc) probe the efficiency of environmentally driven galaxy formation processes and provide direct tests of cosmological predictions \citep[e.g., ][]{kl99ms, moo99ms, stri08commonmass, krav10satrev, kirby10, BKBK11, pontzen12, geha13}. However, searches for faint galaxies suffer from strong luminosity and surface brightness biases that render galaxies with LV ≲ 10⁶ L⊙ difficult to detect beyond the Local Group . Because of these biases, searching for nearby dwarf galaxies with methodologies beyond the standard optical star count methods are essential. This motivates searches for dwarf galaxies using the 21 cm emission line of neutral hydrogen (). While such searches cannot identify passive dwarf galaxies like most Local Group satellites, which lack , they have the potential to find gas-rich, potentially starforming dwarf galaxies. This is exemplified by the case of the Leo P dwarf galaxy, found first in and later confirmed via optical imaging . Here we describe two faint dwarf galaxies identified via emission in the first data release of the Galactic Arecibo L-band Feed Array (GALFA-HI) survey . As described below, they are likely within the Local Volume (<10 Mpc) but just beyond the Local Group (≳1 Mpc), so we refer to them as Pisces A and B. This paper is organized as follows: in Section [sec:data], we present the data used to identify these galaxies. In Section [sec:distance], we consider possible distance scenarios, while in Section [sec:conc] we provide context and some conclusions. Where relevant, we adopt a Hubble constant of $H_0=69.3 \; {\rm km \; s}^{-1}{\rm Mpc}^{-1}$ from WMAP9 .
Swabs to Genomes: A Comprehensive Workflow
Jenna M. Lang
David Coil

Jenna M. Lang

and 6 more

April 12, 2014
Abstract The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
Predictions for Observing Protostellar Outflows with ALMA
Christopher
Stella Offner

Christopher

and 2 more

March 31, 2014
INTRODUCTION Young protostars are observed to launch energetic collimated bipolar mass outflows . These protostellar outflows play a fundamental role in the star formation process on a variety of scales. On sub-pc scales they entrain and unbind core gas, thus setting the efficiency at which dense gas turns into stars . Interaction between outflows and infalling material may regulate protostellar accretion and, ultimately, terminate it . On sub-pc up to cloud scales, outflows inject substantial energy into their surroundings, potentially providing a means of sustaining cloud turbulence over multiple dynamical times. The origin of outflows is attributed to the presence of magnetic fields, and a variety of different models have been proposed to explain the launching mechanism \citep[e.g.,][]{arce07}. Of these, the “disk-wind" model , in which the gas is centrifugally accelerated from the accretion disk surface, and the “X-wind" model , in which gas is accelerated along tightly wound field lines, are most commonly invoked to explain observed outflow signatures. However, investigating the launching mechanism is challenging because launching occurs on scales of a few stellar radii and during times when the protostar is heavily extincted by its natal gas. Consequently, separating outflow gas from accreting core gas, discriminating between models, and determining fundamental outflow properties are nontrivial. Three main approaches have been applied to studying outflows. First, single-dish molecular line observations have been successful in mapping the extent of outflows and their kinematics on core to cloud scales \citep[][]{bourke97,arce10,dunham14}. However, outflow gas with velocities comparable to the cloud turbulent velocity can only be extracted with additional assumptions and modeling \citep[e.g.,][]{arce01b,dunham14}, which are difficult to apply to confused, clustered star forming environments . Second, interferometry provide a means of mapping outflows down to 1,000 AU scales scales , and the Atacama Large Millimeter/submilllimeter Antenna (ALMA) is extending these limits down to sub-AU scales . However, interferometry is not suitable for producing large high-resolution maps and it resolves out larger scale structure. Consequently, it is difficult to assemble a complete and multi-scale picture of outflow properties with these observations. Finally, numerical simulations provide a complementary approach that supplies three-dimensional predictions for launching, entrainment and energy injection . The most promising avenue for understanding outflows lies at the intersection of numerical modeling and observations. By performing synthetic observations to model molecular and atomic lines, continuum, and observational effects, simulations can be mapped into the observational domain where they can be compared directly to observations \citep[e.g.,][]{Offner11,Offner12b,Mairs13}. Such direct comparisons are important for assessing the “reality" of the simulations, to interpret observational data and to assess observational uncertainties . In addition to observational instrument limitations, chemistry and radiative transfer introduce additional uncertainties that are difficult to quantify without realistic models . Synthetic observations have previously been performed in the context of understanding outflow opening angles , observed morphology , and impact on spectral energy distributions . The immanent completion of ALMA provides further motivation for predictive synthetic observations. Although ALMA will have unprecedented sensitivity and resolution compared to existing instruments, by nature interferometry resolves out large-scale structure and different configurations will be sensitive to different scales. Atmospheric noise and total observing time may also effect the fidelity of the data. Previous synthetic observations performed by suggest that the superior resolution of full ALMA and the Atacama Compact Array (ACA) will be able to resolve core structure and fragmentation prior to binary formation. predicts that ALMA will be able to resolve complex outflow velocity structure and helical structure in molecular emission. In this paper we seek to quantify the accuracy of different ALMA configurations in recovering fundamental gas properties such as mass, line-of-sight momentum, and energy. We use the casa software package to synthetically observe protostellar outflows in the radiation-hydrodynamic simulations of . By modeling the emission at different times, inclinations, molecular lines, and observing configurations we evaluate how well physical quantities can be measured in the star formation process. In section §[Methods] we describe our methods for modeling and observing outflows. In section §[results] we evaluate the effects of different observational parameters on bulk quantities. We discuss results and summarize conclusions in §[Conclusions].
Quaternion Based Metrics in Relativity
Benedict Irwin

Benedict Irwin

November 02, 2020
ABSTRACT By introducing a new form of metric tensor the same derivation for the electromanetic tensor Fμν from potentials Aμ leads to the dual space (Hodge Dual) of the regular Fμν tensor. There are additional components in the i, j, k planes, however if after the derivation only the real part is considered a physically consistent electromagnetic theory is recovered with a relabelling of $$ fields to $$ fields and vice versa.
The Microbes We Eat
Jenna M. Lang
Jonathan A. Eisen

Jenna M. Lang

and 2 more

March 04, 2014
ABSTRACT 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 \(1.3 X 10^9\) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at \(6 X 10^6 \)and \(1.4 X 10^6\) 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.
PRECISION ASTEROSEISMOLOGY OF THE WHITE DWARF GD 1212 USING A TWO-WHEEL CONTROLLED KE...
JJ Hermes
Fergal Mullally

JJ Hermes

and 10 more

February 20, 2014
We present a preliminary analysis of the cool pulsating white dwarf GD1212, enabled by more than 11.5 days of space-based photometry obtained during an engineering test of a two-reaction wheel controlled _Kepler_ spacecraft. We detect at least 21 independent pulsation modes, ranging from 369.8 − 1220.8s, and at least 17 nonlinear combination frequencies of those independent pulsations. Our longest uninterrupted light curve, 9.0 days in length, evidences coherent difference frequencies at periods inaccessible from the ground, up to 14.5hr, the longest-period signals ever detected in a pulsating white dwarf. These results mark some of the first science to come from a two-wheel controlled _Kepler spacecraft_, proving the capability for unprecedented discoveries afforded by extending _Kepler_ observations to the ecliptic.
Making Materials Science and Engineering Data More Valueable Research Products
James A Warren
Charles H. Ward

James A Warren

and 2 more

February 17, 2014
Both the global research community and federal governments are embracing a move toward more open sharing of the products of research. Historically, the primary product of research has been the peer-reviewed journal article for fundamental research and government technical report for applied research and engineering for government sponsored research. However, advances in information technology, new “open access” business models, and government policies are working to make publications and supporting materials much more accessible to the general public. These same drivers are obscuring the distinction between the data generated through the course of research and the associated publications. These developments have the potential to significantly enhance the value of both publications and the supporting digital research data, turning them into valuable assets that can be shared and reused by other researchers. The confluence of these shifts in the research landscape leads one to the conclusion that technical publications and their supporting research data must become bound together in a rational fashion. However, bringing these two research products together will require establishment of new policies and a supporting data infrastructure that have essentially no precedent in the materials community, and indeed are stressing many other fields of research. This document raises the key issues that must be addressed in developing these policies and infrastructure, and suggests a path forward in creating the solutions.
Implementing Improved Algorithms for Asteroid Shape Reconstruction using Radar Images
adam greenberg

adam greenberg

February 13, 2014
I present the progress that has been made towards implementing a Square Root Information Filter (SRIF) into the asteroid-modelling software SHAPE. I compare SRIF’s performance with the current fitting algorithm, with the conclusion that SRIF has the potential to perform substantially better than its predecessor. I show the results of SRIF operating on previously collected delay-doppler data for the asteroid 2000 ET70. I also discuss potential future changes to improve shape’s fitting speed and accuracy.
Manifold Warping: Manifold Alignment Over Time
CJ Carey

CJ Carey

February 01, 2014
Knowledge transfer is computationally challenging, due in part to the curse of dimensionality, compounded by source and target domains expressed using different features (e.g., documents written in different languages). Recent work on manifold learning has shown that data collected in real-world settings often have high-dimensional representations, but lie on low-dimensional manifolds. Furthermore, data sets collected from similar generating processes often present different high-dimensional views, even though their underlying manifolds are similar. The ability to align these data sets and extract this common structure is critical for many transfer learning tasks. In this paper, we present a novel framework for aligning two sequentially-ordered data sets, taking advantage of a shared low-dimensional manifold representation. Our approach combines traditional manifold alignment and dynamic time warping algorithms using alternating projections. We also show that the previously-proposed canonical time warping algorithm is a special case of our approach. We provide a theoretical formulation as well as experimental results on synthetic and real-world data, comparing manifold warping to other alignment methods.
Photometric Science Alerts From Gaia
Heather Campbell

Heather Campbell

January 30, 2014
Gaia is a European Space Agency (ESA) astrometry space mission, and a successor to the ESA Hipparcos mission. The main goal of the Gaia mission is to collect high-precision astrometric data (i.e. positions, parallaxes, and proper motions) for the brightest one billion objects in the sky. This data, complemented with G band, multi-epoch photometric and low resolution (lowers) spectroscopic data collected from the same observing platform, will allow astronomers to reconstruct the formation history, structure, and evolution of the Galaxy. In addition, the Gaia satellite is an excellent transient discovery instrument, covering the whole sky (including the Galactic plane) for the next 5 years, at high spatial resolution (50 to 100 mas, similar to the Hubble space telescope (HST)) with precise photometry (1% at G=19) and milliarcsecond astrometry (down to ∼20mag). Thus, Gaia provides a unique opportunity for the discovery of large numbers of transient and anomalous events, e.g. supernovae, black hole binaries and tidal disruption events. We discuss the validation of the alerts stream for the first six months of the Gaia observations, in particular noting how a significant ground based campaign involving photometric and spectroscopic followup of early Gaia alerts is now in place. We discuss the validation approach, and highlight in more detail the specific case of Type Ia supernova (SNe Ia) to be discovered by Gaia. The intense initial ground based validation campaign will ensure that the Gaia alerts stream for the remainder of the Gaia mission, are well classified.
Solar radiation exposure of dihydrobiopterin and biopterin in aqueous solution
Adriana Ipiña
Andrés H. Thomas

Adriana Ipiña

and 3 more

December 09, 2013
Dihydrobiopterin (H₂Bip) and biopterin (Bip) accumulate in the skin of patients suffering from vitiligo, whose lack of melanin causes a deficient protection against UV radiation. H₂Bip and Bip undergo photooxidation upon UV irradiation and the former acts as a photosensitizer of biomolecules. The aim of this work is to study the photochemical reactions of these compounds triggered by sunlight under outdoor conditions. H₂Bip and Bip in aqueous solutions were exposed to sunlight in La Plata city (34.90∘S, 57.92∘W) from Spring equinox to near Summer solstice and the spectral solar irradiance was recorded with a high-resolution spectrometer. The photochemical reactions were followed by HPLC and UV-Vis spectrophotometry. Upon sun exposure, excitation of H₂Bip leads to the formation of dimers and to its oxidation to Bip, which, in turn, is photooxidized into 6-formylpterin (Fop). Further excitation induces the oxidation of Fop to 6-carboxypterin, which is much more photostable than Bip and Fop and then it is accumulated in the solution. Rates of reactant consumption were determined under different weather conditions and the corresponding quantum yields were also calculated. We have demonstrated that solar radiation causes significant oxidation of the pterin derivatives investigated within a few minutes, even in cloudy days. Finally, the biological implications of our results are discussed.
Influence of Depth of Interaction upon the Performance of Scintillator Detectors
Mark S. Brown
Stefan

Mark S. Brown

and 6 more

December 02, 2013
The uncertainty in time of particle detection within a scintillator detector, characterised by the coincidence time resolution (CTR), is explored with respect to the interaction position within the scintillator crystal itself. Electronic collimation between two scintillator detectors is utilised to determine the CTR with depth of interaction (DOI) for different materials, geometries and wrappings. Significantly, no relationship between the CTR and DOI is observed within experimental error. Confinement of the interaction position is seen to degrade the CTR in long scintillator crystals by 10%.
Unearthing the contributions and ecology of uncultured soil bacteria to the metabolis...
Ashley Campbell
Charles Pepe-Ranney

Ashley Campbell

and 2 more

November 25, 2013
INTRODUCTORY PARAGRAPH We explored the microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either ¹³C-xylose or ¹³C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for ¹³C-incorporation into DNA from ¹³C-xylose and ¹³C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated ¹³C in the ¹³C-xylose treatment changed over time being predominantly _Firmicutes_ at day 1 followed by _Bacteroidetes_ at day 3 and then _Actinobacteria_ at day 7. These ¹³C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including _Verrucomicrobia_, _Chloroflexi_ and _Planctomycetes_.
10 Simple Rules for the Care and Feeding of Scientific Data
Alberto Pepe
Alyssa Goodman

Alberto Pepe

and 1 more

November 10, 2013
INTRODUCTION In the early 1600s, Galileo Galilei turned a telescope toward Jupiter. In his log book each night, he drew to-scale schematic diagrams of Jupiter and some oddly-moving points of light near it. Galileo labeled each drawing with the date. Eventually he used his observations to conclude that the Earth orbits the Sun, just as the four Galilean moons orbit Jupiter. History shows Galileo to be much more than an astronomical hero, though. His clear and careful record keeping and publication style not only let Galileo understand the Solar System, it continues to let _anyone_ understand _how_ Galileo did it. Galileo’s notes directly integrated his DATA (drawings of Jupiter and its moons), key METADATA (timing of each observation, weather, telescope properties), and TEXT (descriptions of methods, analysis, and conclusions). Critically, when Galileo included the information from those notes in _Siderius Nuncius_ , this integration of text, data and metadata was preserved, as shown in Figure 1. Galileo's work advanced the "Scientific Revolution," and his approach to observation and analysis contributed significantly to the shaping of today's modern "Scientific Method" . Today most research projects are considered complete when a journal article based on the analysis has been written and published. Trouble is, unlike Galileo's report in _Siderius Nuncius_, the amount of real data and data description in modern publications is almost never sufficient to repeat or even statistically verify a study being presented. Worse, researchers wishing to build upon and extend work presented in the literature often have trouble recovering data associated with an article after it has been published. More often than scientists would like to admit, they cannot even recover the data associated with their own published works. Complicating the modern situation, the words "data" and "analysis" have a wider variety of definitions today than at the time of Galileo. Theoretical investigations can create large "data" sets through simulations (e.g. The Millennium Simulation Project). Large scale data collection often takes place as a community-wide effort (e.g. The Human Genome project), which leads to gigantic online "databases" (organized collections of data). Computers are so essential in simulations, and in the processing of experimental and observational data, that it is also often hard to draw a dividing line between "data" and "analysis" (or "code") when discussing the care and feeding of "data." Sometimes, a copy of the code used to create or process data is so essential to the use of those data that the code should almost be thought of as part of the "metadata" description of the data. Other times, the code used in a scientific study is more separable from the data, but even then, many preservation and sharing principles apply to code just as well as they do to data. So how do we go about caring for and feeding data? Extra work, no doubt, is associated with nurturing your data, but care up front will save time and increase insight later. Even though a growing number of researchers, especially in large collaborations, know that conducting research with sharing and reuse in mind is essential, it still requires a paradigm shift. Most people are still motivated by piling up publications and by getting to the next one as soon as possible. But, the more we scientists find ourselves wishing we had access to extant but now unfindable data , the more we will realize why bad data management is bad for science. How can we improve? THIS ARTICLE OFFERS A SHORT GUIDE TO THE STEPS SCIENTISTS CAN TAKE TO ENSURE THAT THEIR DATA AND ASSOCIATED ANALYSES CONTINUE TO BE OF VALUE AND TO BE RECOGNIZED. In just the past few years, hundreds of scholarly papers and reports have been written on questions of data sharing, data provenance, research reproducibility, licensing, attribution, privacy, and more--but our goal here is _not_ to review that literature. Instead, we present a short guide intended for researchers who want to know why it is important to "care for and feed" data, with some practical advice on how to do that. The set of Appendices at the close of this work offer links to the types of services referred to throughout the text. BOLDFACE LETTERING below highlights actions one can take to follow the suggested rules.
Molecular tools for synthetic biology in plants: a first generation open bioinformati...
Ron Shigeta
Jamey

Ron Shigeta

and 6 more

August 29, 2013
Synthetic biology has had profound effects on human life. It has provided more effective anti-malarial medicine, cheaper insulin, new useful bio-materials, and greener biofuels. However, much remains to be learned in order to synthesize proteins more efficiently. To explore the potential of the DIY biology movement to engage in meaningful synthetic biology bioinformatics research, we developed a bioinformatics workshop to study determinants of protein expression levels in plants. We extracted possible ribosome binding and translation initiation sequences and looked for correlations with experimentally determined protein levels, using publicly available data sets for the widely studied plants _Oryza sativa_ and _Arabidopsis thaliana_. The working group was open to the public and met every other week for 3 hours, typically starting with a short, relevant presentation followed by hands-on data work. We aim to develop, experimentally validate, and publish our consensus sequences, anticipating that our work will be useful for plant synthetic biology research. We hope our experience will serve as a model for future community projects that serve the dual purpose of educating curious members of the public while also generating useful scientific results.
First Look at the Physics Case of TLEP
Patrick Janot
Patrizia Azzi

Patrick Janot

and 14 more

August 28, 2013
INTRODUCTION The Higgs boson with mass around 125 GeV recently discovered by the ATLAS and CMS experiments  at the LHC is found to have properties compatible with the Standard Model predictions , as shown for example in Fig. [fig:ellis] . Coupled with the absence of any other indication so far for new physics at the LHC, be it either through precision measurements or via direct searches, this fundamental observation seems to push the energy scale of any physics beyond the Standard Model above several hundred GeV. The higher-energy LHC run, which is expected to start in 2015 at $ \sim 13$-14 TeV, will extend the sensitivity to new physics to 1 TeV or more. Fundamental discoveries may therefore be made in this energy range by 2017-2018. Independently of the outcome of this higher-energy run, however, there must be new phenomena, albeit at unknown energy scales, as shown by the evidence for non-baryonic dark matter, the cosmological baryon-antibaryon asymmetry and non-zero neutrino masses, which are all evidence for physics beyond the Standard Model. In addition to the high-luminosity upgrade of the LHC, new particle accelerators will be instrumental to understand the physics underlying these observations.
KIC 9246715: The Double Red Giant Eclipsing Binary With Odd Oscillations
Meredith L. Rawls
patrick gaulme

Meredith L. Rawls

and 9 more

August 19, 2013
We combine _Kepler_ photometry with ground-based spectra to present a comprehensive dynamical model of the double red giant eclipsing binary KIC 9246715. While the two stars are very similar in mass ($M_1 = 2.171 \ M_{\odot}$, $M_2 = 2.149 \ M_{\odot}$) and radius ($R_1 = 8.37 \ R_{\odot}$, $R_2 = 8.30 \ R_{\odot}$), an asteroseismic analysis finds one main set of solar-like oscillations with unusually low-amplitude, wide modes. A second set of oscillations from the other star may exist, but this marginal detection is extremely faint. Because the two stars are nearly twins, KIC 9246715 is a difficult target for a precise test of the asteroseismic scaling relations, which yield M = 2.17 ± 0.14 M⊙ and R = 8.26 ± 0.18 R⊙. Both stars are consistent with the inferred asteroseismic properties, but we suspect the main oscillator is Star 2 because it is less active than Star 1. We find evidence for stellar activity and modest tidal forces acting over the 171-day eccentric orbit, which are likely responsible for the essential lack of solar-like oscillations in one star and weak oscillations in the other. Mixed modes indicate the main oscillating star is on the secondary red clump (a core-He-burning star), and stellar evolution modeling supports this with a coeval history for a pair of red clump stars. This system is a useful case study and paves the way for a detailed analysis of more red giants in eclipsing binaries, an important benchmark for asteroseismology.
Mission Possible: Using visual feedback to improve physical activity in children
Gerrit Niezen
Kelly Mackintosh

Gerrit Niezen

and 3 more

August 06, 2013
This paper describes the deployment of a novel ubiquitous behaviour change system for social interaction and reflection amongst school children. For four weeks, a class of schoolchildren (Year 5) was monitored with Fitbit activity monitors and their daily physical activity was visualised on a custom ambient display. In addition, video segments describing mission-based activities were shown on tablet devices to the children at the start of each week. The ambient display would indicate if they performed better than the previous day. We describe how the system was designed and developed, present findings from the in-the-wild study, and provide design guidelines for future studies.
← Previous 1 2 … 1927 1928 1929 1930 1931 1932 1933 1934 1935 Next →
Authorea
  • Home
  • About
  • Product
  • Preprints
  • Pricing
  • Blog
  • Twitter
  • Help
  • Terms of Use
  • Privacy Policy