Evaluating and promoting open data practices in open access journals

The last decade has seen a dramatic increase in attention from the scholarly communications and research community to open access (OA) and open data practices. These are potentially related because journal publication policies and practices both signal disciplinary norms and provide direct incentives for data sharing and citation. However, there is little research evaluating the data policies of OA journals. In this study we analyse the state of data policies for OA journals by employing random sampling of the Directory of Open Access Journals and Open Journal Systems journal directories and applying a coding framework that integrates both previous studies and emerging taxonomies of data sharing and citation. This study, for the first time, reveals both the low prevalence of datasharing policies and practices in OA journals, which differs from the previous studies of commercial journals in specific disciplines

On the Peripheries of Scholarly Infrastructure: A Look at the Journals Using Open Journal Systems

The Public Knowledge Project (PKP) is a research and development initiative of Simon Fraser University and Stanford University, with a focus on understanding and building enhanced modes of scholarly communication that facilitate open access, high quality publishing, and local capacity building and participation. One of the most significant contributions from PKP has been the development of its free, open source Open Journal Systems (OJS) software. Although some existing publishers have made use of the system, the majority of OJS users are new to publishing and are based in academia, either through library publishing programs or by individual "scholar-publishers," determined to build communities of interest around their research areas (Edgar & Willinsky, 2010). Most are small-scale, often operating with in-kind contributions and minimal budgets (Edgar & Willinsky, 2010). This type of use suggests an increased participation in scholarship, both in terms of who publishes and who read

Selected Information Management Resources for Implementing New Knowledge Environments: An Annotated Bibliography

This annotated bibliography reviews scholarly work in the area of building and analyzing digital document collections with the aim of establishing a baseline of knowledge for work in the field of digital humanities. The bibliography is organized around three main topics: data stores, text corpora, and analytical facilitators. Each of these is then further divided into sub-topics to provide a broad snapshot of modern information management techniques for building and analyzing digital documents collections

Introducing Texture: An Open Source WYSIWYG Javascript Editor for JATS

Texture is a WYSIWYG editor app that allows users to turn raw content into structured content, and add as much semantic information as needed for the production of scientific publications. Texture is open source software built on top of Substance (http://substance.io), an advanced Javascript content authoring library. While the Substance library is format agnostic, the Texture editor uses JATS XML as a native exchange format. The Substance library that Texture is built on already supports real-time collaborative authoring, and the easy-to-use WYSIWYG interface would make Texture an attractive alternative to Google Docs. For some editors, the interface could be toggled to more closely resemble a professional XML suite, allowing a user to pop out a raw attribute editor for any given element. Textureauthored documents could then be brought into the journal management system directly, skipping the conversion step, and move straight into a document-centric publishing workflow. &nbsp

Building a Bridge Between Journal Articles and Research Data: The PKP-Dataverse Integration Project

A growing number of funding agencies and international scholarly organizations are requesting that research data be made more openly available to help validate and advance scientific research. Thus, this is an opportune moment for research data repositories to partner with journal editors and publishers in order to simplify and improve data curation and publishing practices. One practical example of this type of cooperation is currently being facilitated by a two year (2012-2014) one million dollar Sloan Foundation grant, integrating two well-established open source systems: the Public Knowledge Project’s (PKP) Open Journal Systems (OJS), developed by Stanford University and Simon Fraser University; and Harvard University’s Dataverse Network web application, developed by the Institute for Quantitative Social Science (IQSS). To help make this interoperability possible, an OJS Dataverse plugin and Data Deposit API are being developed, which together will allow authors to submit their articles and datasets through an existing journal management interface, while the underlying data are seamlessly deposited into a research data repository, such as the Harvard Dataverse. This practice paper will provide an overview of the project, and a brief exploration of some of the specific challenges to and advantages of this integration

Fructose transport-deficient Staphylococcus aureus reveals important role of epithelial glucose transporters in limiting sugar-driven bacterial growth in airway surface liquid.

Hyperglycaemia as a result of diabetes mellitus or acute illness is associated with increased susceptibility to respiratory infection with Staphylococcus aureus. Hyperglycaemia increases the concentration of glucose in airway surface liquid (ASL) and promotes the growth of S. aureus in vitro and in vivo. Whether elevation of other sugars in the blood, such as fructose, also results in increased concentrations in ASL is unknown and whether sugars in ASL are directly utilised by S. aureus for growth has not been investigated. We obtained mutant S. aureus JE2 strains with transposon disrupted sugar transport genes. NE768(fruA) exhibited restricted growth in 10 mM fructose. In H441 airway epithelial-bacterial co-culture, elevation of basolateral sugar concentration (5-20 mM) increased the apical growth of JE2. However, sugar-induced growth of NE768(fruA) was significantly less when basolateral fructose rather than glucose was elevated. This is the first experimental evidence to show that S. aureus directly utilises sugars present in the ASL for growth. Interestingly, JE2 growth was promoted less by glucose than fructose. Net transepithelial flux of D-glucose was lower than D-fructose. However, uptake of D-glucose was higher than D-fructose across both apical and basolateral membranes consistent with the presence of GLUT1/10 in the airway epithelium. Therefore, we propose that the preferential uptake of glucose (compared to fructose) limits its accumulation in ASL. Pre-treatment with metformin increased transepithelial resistance and reduced the sugar-dependent growth of S. aureus. Thus, epithelial paracellular permeability and glucose transport mechanisms are vital to maintain low glucose concentration in ASL and limit bacterial nutrient sources as a defence against infection

Final Report: ASIS&T Task Force on Webinars

This report was submitted to the American Society for Information Science and Technology (ASIS&T) Board of Directors. In June 2011, an ASIS&T Task Force on Webinars was appointed. This is the final report discusses the findings of this task force and recommendations

Oxygen Metallicity Determinations from Optical Emission Lines in Early-type Galaxies

We measured the oxygen abundances of the warm (T$\sim 10^{4}K$) phase of gas in seven early-type galaxies through long-slit observations. A template spectra was constructed from galaxies void of warm gas and subtracted from the emission-line galaxies, allowing for a clean measurement of the nebular lines. The ratios of the emission lines are consistent with photoionization, which likely originates from the UV flux of post-asymototic giant branch (PAGB) stars. We employ H II region photoionization models to determine a mean oxygen metallicity of $1.01\pm0.50$ solar for the warm interstellar medium (ISM) in this sample. This warm ISM 0.5 to 1.5 solar metallicity is consistent with modern determinations of the metallicity in the hot (T$\sim 10^{6}-10^{7}K$) ISM and the upper range of this warm ISM metallicity is consistent with stellar population metallicity determinations. A solar metallicity of the warm ISM favors an internal origin for the warm ISM such as AGB mass loss within the galaxy.Comment: Accepted Astrophysical Journa

Toward Modeling the Social Edition: An Approach to Understanding the Electronic Scholarly Edition in the Context of New and Emerging Social Media

This article explores building blocks in extant and emerging social media toward the possibilities they offer to the scholarly edition in electronic form, positing that we are witnessing the nascent stages of a new ‘social’ edition existing at the intersection of social media and digital editing. Beginning with a typological formulation of electronic scholarly editions, activities common to humanities scholars who engage with texts as expert readers are considered, noting that many methods of engagement both reflect the interrelated nature of long-standing professional reading strategies and are social in nature; extending this frame work, the next steps in the scholarly edition’s development in its incorporation of social media functionality reflect the importance of traditional humanistic activities and workflows, and include collaboration, incorporating contributions by its readers and re-visioning the role of the editor away from that of ultimate authority and more toward that of facilitator of reader involvement. Intended to provide a ‘toolkit’ for academic consideration, this discussion of the emerging social edition points to new methods of textual engagement in digital literary studies and is accompanied by two integral, detailed appendices, published in Digital Humanities Quarterly under the title ‘Pertinent discussions toward modeling the social edition: Annotated bibliographies’ (http://www.digitalhumanities.org/dhq/vol/6/1/000111/000111.html): one addressing issues pertinent to online reading and interaction, and another on social networking tools

Radiocarbon data reveal contrasting sources for carbon fractions in thermokarst lakes and rivers of Eastern Canada (Nunavik, Quebec)

Greenhouse gas (GHG) emissions from permafrost organic carbon decomposition in lakes and rivers can accelerate global warming. We used radiocarbon (14C) measurements to determine the predominant sources of dissolved organic carbon (DOC), particulate organic carbon (POC), dissolved inorganic carbon (DIC), and methane (CH4) in five thermokarst lakes and three rivers in an area of widespread permafrost degradation in Northern Quebec to assess contributions from thawing permafrost and other old carbon (fixed before CE 1950) reservoirs. We compared emission pathways (dissolved gas and ebullition), seasons (summer and winter), and surface soil type (mineral and peat soils). Modern carbon (fixed after CE 1950) was the dominant source of DOC, DIC, and CH4 of non‐peatland aquatic systems, while POC and sediment carbon were predominantly fixed in the last millennia. In the peatland systems, modern and permafrost carbon were important sources of DOC, lake DIC, lake ebullition CO2, and lake dissolved CH4. In contrast, POC, lake ebullition CH4, and river DIC were dominated by millennial‐old carbon. In winter, the 14C age of DOC, DIC, and POC in the peatland lakes increased, but the 14C age of dissolved CH4 did not change. Our results point to a clearly older overall carbon source for ebullition CH4 relative to dissolved CH4 in the peatland lakes, but not the non‐peatland lakes. The younger ages of diffusive CH4 and DIC relative to DOC and POC in all lakes suggest that recent primary productivity strongly influences the large total lake CH4 emissions in this area, as diffusion fluxes greatly exceed ebullition fluxes