Humanities Commons Open Repository Exchange

The Modern Language Association (MLA) and the Columbia University Libraries / Information Services' Center for Digital Research and Scholarship (CDRS) have been working together on a prototyped user interface that connects a library-quality repository system (Humanities Commons Open Repository Exchange, or CORE, modeled on Columbia's Academic Commons) with MLA Commons, an academic social networking platform that enables MLA members to communicate, collaborate, and share their work with one another. The CORE interface allows Commons members to upload, share, discover, retrieve, and archive digital work and other objects in an existing collaboratory network. This white paper describes the team's progress and setbacks over the grant period

Building Tremor Journal: Examining the Costs of Open Access Publishing

The Center for Digital Research and Scholarship (CDRS) was established in 2007 by the Columbia University Libraries/ Information Services (CUL/IS) to explore and provision new research support services for the university in all areas of scholarly communication, including online scholarly publishing. (Renfro and Neal, 2012) As the landscape for library publishing has continued to grow, CDRS has found an increasing level of demand for library-based support of publishing initiatives from within the University and beyond. Because of CDRS’ unique position as an organization housed within the existing CUL/IS infrastructure, the Center has access to a great deal of resources and support systems that have enabled it to provide a full suite of services in support of library-based publishing, including the publication of Tremor and Other Hyperkinetic Movements (TOHM) journal (http://www.tremorjournal.org/), a fully open access scientific journal based on the Open Journal Systems (OJS) software. Using CDRS' publication and support of TOHM as a case study, this presentation will examine the costs involved in publishing an open access journal, moving beyond the basic setup and execution of a journal website capable of incorporating a peer-review workflow to look in detail at the specific essential services CDRS provides, including: Software development, hosting, and maintenance: The Center continually works to develop on top of the OJS software to customize the web site to allow for full journal publication workflow, including the build of a plugin to work with third-party vendors. Indexing support: In an effort to uphold the journal’s contribution to the scientific community, CDRS has successfully undertaken application for indexing in PubMed Central (http://www.ncbi.nlm.nih.gov/pmc/), and continues to maintain this relationship. Finance management: Through the Center’s relationship with the library finance office, CDRS manages the journal’s finances, including author fees, waivers, and the incorporation of third-party funding and grants to the journal. Research and Development: A constant aspect of CDRS’ support for open-access publication through TOHM is the task of keeping abreast of new opportunities for enhancing the scholarly content through new software tools and platforms; metadata optimization and SEO tools; and methods for integration with the broader scientific research community. The support of TOHM speaks to the Center’s strategy for securing paths for the open access to scholarly research. Additionally, as exemplified by the Library Publishing Coalition’s (LPC) goal to “refine justification and positioning for library-based publishing activities,” (“LPC Project Deliverables”) it provides a useful mechanism for analysis of the opportunities the greater research library community has in the support of scholarly research publication

Emerging Opportunities in Library Services: Planning for the Future of Scholarly Publishing

In 2007, the Columbia University Libraries/Information Services (CUL/IS) established the Center for Digital Research and Scholarship (CDRS) to explore and provision new research support services for the university in all areas of scholarly communication, including online scholarly publishing. One of six organizations comprising the Digital Programs and Technology Services group within CUL/IS, CDRS assists faculty, students, staff, and university affiliates with their scholarly communication and digital research needs through a suite of services: publishing support, digital research repository, conference websites and video recording, research data management, and more. Nine of its 17 full-time employees belong to a production team comprising developers, designers, and project managers from diverse academic and professional backgrounds, only one of whom holds a master’s degree in library science. CDRS seeks publishing partnerships with a variety of on-campus groups and individuals and embraces partnerships with allied organizations such as scholarly presses and societies as well. A proponent of eliminating barriers to the progress of research, CDRS advocates for open access (OA) publishing models. This is exemplified by Tremor and Other Hyperkinetic Movements, the peer-reviewed, faculty-run OA journal now indexed in PubMed, which CDRS publishes. To help offset the OA journal publication costs, Tremor authors pay an article processing fee, although waivers and alternative methods of funding are available. In practice, CDRS’ approach to publishing support is business model–neutral, however,and OA is not a requirement for partnership. The journals program at CDRS has been successful, providing publishing support to 16 journals using the Open Journal Systems or WordPress platforms and interactive tools such as blogs and wikis in subject areas ranging from sciences to the humanities. A strategy for keeping this service sustainable and scalable has been the adoption of a tiered structure based on design and customization needs to control flow. Projects can take anywhere from one week for a barebones installation to over 17 weeks for the Premier service

New Partnerships in the Scholarly Communication System and the Open Source Toolkit

Community-supported open source projects such as Hydra, Fedora and Blacklight create opportunities for collective advancement and strategic support and sustainability for essential digital library infrastructure. Commitment to and participation in the development of stable platforms, however, opens and strengthens partnerships for libraries and their collaborators. Reciprocally, partnerships built on such platforms expand the range of potential use cases and feed back neatly into the community development model. The Center for Digital Research and Scholarship (CDRS) at Columbia University Libraries has been developing project-based partnerships with allied groups in the broader landscape of scholarly communication that draw upon the organizational commitments to contribute to the growth and proliferation of these platforms. CDRS and its partners attained two related project milestones in 2015: (1) The Modern Language Association and CDRS completed an NEH-funded pilot project (HumCORE) to couple digital research repository technology and service infrastructure with a society-supported disciplinary-focused community hub for scholars; (2) In partnership with the Columbia University Press, the Columbia Libraries refreshed the search and discovery interface for the Columbia International Affairs Online (CIAO) database. The presenters will explore the rationale that led to the development of these projects and the infrastructure choices made to support them. The presenters will also explore the hoped-for impacts and effects of such projects as they may inform use case development for the open source projects themselves

Deep three-dimensional solid-state qubit arrays with long-lived spin coherence

Nitrogen-vacancy centers (NVCs) in diamond show promise for quantum computing, communication, and sensing. However, the best current method for entangling two NVCs requires that each one is in a separate cryostat, which is not scalable. We show that single NVCs can be laser written 6–15-µm deep inside of a diamond with spin coherence times that are an order of magnitude longer than previous laser-written NVCs and at least as long as naturally occurring NVCs. This depth is suitable for integration with solid immersion lenses or optical cavities and we present depth-dependent T2 measurements. 200 000 of these NVCs would fit into one diamond

Quantifying full phenological event distributions reveals simultaneous advances, temporal stability and delays in spring and autumn migration timing in long-distance migratory birds

Acknowledgements We thank all Fair Isle Bird Observatory staff and volunteers for help with data collection and acknowledge the foresight of George Waterston and Ken Williamson in instigating the observatory and census methodology. We thank all current and previous directors of Fair Isle Bird Observatory Trust for their contributions, particularly Dave Okill and Mike Wood for their stalwart support for the long-term data collection and for the current analyses. Dawn Balmer and Ian Newton provided helpful guidance on manuscript drafts. We thank Ally Phillimore and two anonymous referees for helpful comments. This study would have been impossible without the Fair Isle community's invaluable support and patience over many decades, which is very gratefully acknowledged. WTSM and JMR designed and undertook analyses, wrote the paper and contributed to data collection and compilation, MB contributed to analysis and editing, all other authors oversaw and undertook data collection and compilation and contributed to editing.Peer reviewedPostprin

In vivo parasitological measures of artemisinin susceptibility

Parasite clearance data from 18,699 patients with falciparum malaria treated with an artemisinin derivative in areas of low (n=14,539), moderate (n=2077), and high (n=2083) levels of malaria transmission across the world were analyzed to determine the factors that affect clearance rates and identify a simple in vivo screening measure for artemisinin resistance. The main factor affecting parasite clearance time was parasite density on admission. Clearance rates were faster in high-transmission settings and with more effective partner drugs in artemisinin-based combination treatments (ACTs). The result of the malaria blood smear on day 3 (72 h) was a good predictor of subsequent treatment failure and provides a simple screening measure for artemisinin resistance. Artemisinin resistance is highly unlikely if the proportion of patients with parasite densities of <100,000 parasites/microL given the currently recommended 3-day ACT who have a positive smear result on day 3 is <3%; that is, for n patients the observed number with a positive smear result on day 3 does not exceed (n + 60)/24

Low and High Birth Weights Are Risk Factors for Nonalcoholic Fatty Liver Disease in Children

OBJECTIVES: To examine the distribution of birth weight in children with nonalcoholic fatty liver disease (NAFLD) compared with the general US population, and to investigate the relationship between birth weight and severity of NAFLD. STUDY DESIGN: A multicenter, cross-sectional study of children with biopsy-proven NAFLD enrolled in the Nonalcoholic Steatohepatitis Clinical Research Network Database. Birth weight was categorized as low birth weight (LBW), normal birth weight (NBW), or high birth weight (HBW) and compared with the birth weight distribution in the general US population. The severity of liver histology was assessed by birth weight category. RESULTS: Children with NAFLD (n = 538) had overrepresentation of both LBW and HBW compared with the general US population (LBW, 9.3%; NBW, 75.8%; HBW, 14.9% vs LBW, 6.1%; NBW, 83.5%; HBW 10.5%; P < .0001). Children with HBW had significantly greater odds of having more severe steatosis (OR, 1.82, 95% CI. 1.15-2.88) and nonalcoholic steatohepatitis (OR, 2.03; 95% CI, 1.21-3.40) compared with children with NBW. In addition, children with NAFLD and LBW had significantly greater odds of having advanced fibrosis (OR, 2.23; 95% CI, 1.08-4.62). CONCLUSION: Birth weight involves maternal and in utero factors that may have long-lasting consequences. Children with both LBW and HBW may be at increased risk for developing NAFLD. Among children with NAFLD, those with LBW or HBW appear to be at increased risk for more severe disease