RIOJA (Repository Interface to Overlaid Journal Archives) project: final report

RIOJA (Repository Interface to Overlaid Journal Archives) was a 18-month partnership between UCL (University College London), Imperial College London, and the Universities Glasgow, Cambridge and Cornell. The project was funded by the JISC (Joint Information Systems Committee, UK). The project team worked with the Astrophysics community investigate aspects of overlay journals. For the purposes of the project, an overlay was defined as a quality-assured journal whose content is deposited to and resides more open access repositories. The project had both technical aims and supporting, non-technical aims. The primary technical deliverable from the project was a toolkit for the creation and maintenance overlay journals. The toolkit supports the exchange of data between a repository and piece of journal software. It supports functions such as author validation, metadata extraction from the source repository, and submission tracking. The toolkit is platform-neutral and could, in theory, be employed by any journal using content from any number repositories, in any discipline. The project also implemented a demonstrator overlay applying the RIOJA toolkit to the arXiv subject repository, and a demonstrator implementation of the RIOJA tool for GNU EPrints. Aside from creating the demonstrator and its underlying tools, the project aimed to acceptibility and feasibility of the overlay model. First, a large-scale survey of the Astrophysics community was undertaken. The survey collected data about research publishing practices within this community, and probed its reaction to the principle publishing. Second, the views of editors and publishers in this discipline were sought through interviews. These views were added to findings from the literature and summarised in a more general report on issues around the sustainability of an overlay journal

The DART-Europe project: towards developing a European theses portal

This paper will report on the new European theses project DART-Europe. The purpose of this project is to align institutional and national e-theses developments across Europe with the wider open archives movement by the construction of a European portal for research theses, thus enabling a global view of European institutional research assets. This project is driven through an innovative partnership between an information provider and an international body of university libraries and open access consortia. The project’s goal is to explore the creation of a European model for the deposit, discovery, use and long-term care of research theses in an open access environment. The paper will outline the projected outcomes of DART-Europe, which is an active group of institutions in addition to a technical service. To this end, DART-Europe is engaged with disciplines and institutions that are widening the definition of research by redefining the formats of theses. For institutions and countries without a repository infrastructure, DART-Europe will enable the creation of a depository. Institutions and countries with a repository infrastructure can engage with DART-Europe to deliver their e-theses. DART-Europe acts as a technology bridge for researchers between those who have existing infrastructures and those who do not. The DART-Europe architecture assumes free at point of use access to full text theses, whether held on the DART-Europe server or by institutional repositories. This paper will provide session attendees with the current progress of this initiative, including a report on the 5 strands of the project, including: architecture; creation of a management tool kit; content acquisition; digital preservation and an investigation of business models

A Molecular Phylogeny of Black-Tyrants (Tyrannidae: Knipolegus) Reveals Strong Geographic Patterns and Homoplasy in Plumage and Display Behavior

This is the Publisher's version, also available from http://www.bioone.org/doi/abs/10.1525/auk.2012.11101.We present the first molecular phylogenetic hypothesis for Knipolegus (black-tyrants), a widespread genus of South American tyrant-flycatchers, based on nuclear and mitochondrial DNA sequences. Bayesian and maximum-likelihood analyses support three clades within Knipolegus, one confined to northern South America, one confined to southeast Brazil, and one confined to the Southern Cone and southern Andes. Within each clade, two or more species are broadly sympatric or parapatric, overlapping in general distribution but differing in habitat specialization. Maximum-likelihood ancestral state reconstructions using an equal-rate stochastic model support a single origin of austral migration in the southern group. Contrasting with these strong geographic patterns, ancestral state reconstructions of plumage and display evolution were more complex, with multiple inferred character-state changes. Ancestral state reconstructions suggest a sexually dimorphic ancestor of Knipolegus, and sexually similar plumages are the result of three independent character-state changes: one in male plumage and two in female plumage. Ancestral state reconstructions support the conclusion that flight displays with mechanical sounds originated in the Knipolegus ancestor, and loss of mechanical sounds in flight displays occurred twice

Assessing Regulatory Impact Analyses: The Failure of Agencies to Comply With Executive Order 12,866

None.Environment, Health and Safety, Regulatory Reform

Assessing the Quality of Regulatory Impact Analyses

This study provides the most comprehensive evaluation of the quality of recent economic analyses that agencies conduct before finalizing major regulations. We construct a new dataset that includes analyses of forty-eight major health, safety, and environmental regulations from mid-1996 to mid-1999. This dataset provides detailed information on a variety of issues, including an agency's treatment of benefits, costs, net benefits, discounting, and uncertainty. We use this dataset to assess the quality of recent economic analyses and to determine the extent to which they are consistent with President Clinton's Executive Order 12866 and the benefit-cost guidelines issued by the Office of Management and Budget (OMB). We find that economic analyses prepared by regulatory agencies typically do not provide enough information to make decisions that will maximize the efficiency or effectiveness of a rule. Agencies quantified net benefits for only 29 percent of the rules. Agencies failed to discuss alternatives in 27 percent of the rules and quantified costs and benefits of alternatives in only 31 percent of the rules. Our findings strongly suggest that agencies generally failed to comply with the executive order and adhere to the OMB guidelines. We offer specific suggestions for improving the quality of analysis and the transparency of the regulatory process, including writing clear executive summaries, making analyses available on the Internet, providing more careful consideration of alternatives to a regulation, and estimating net benefits of a regulation when data on costs and benefits are provided.

Cored in the act: The use of models to understand core myopathies

The core myopathies are a group of congenital myopathies with variable clinical expression - ranging from early-onset skeletal-muscle weakness to later-onset disease of variable severity - that are identified by characteristic 'core-like' lesions in myofibers and the presence of hypothonia and slowly or rather non-progressive muscle weakness. The genetic causes are diverse; central core disease is most often caused by mutations in ryanodine receptor 1 (RYR1), whereas multi-minicore disease is linked to pathogenic variants of several genes, including selenoprotein N (SELENON), RYR1 and titin (TTN). Understanding the mechanisms that drive core development and muscle weakness remains challenging due to the diversity of the excitation-contraction coupling (ECC) proteins involved and the differential effects of mutations across proteins. Because of this, the use of representative models expressing a mature ECC apparatus is crucial. Animal models have facilitated the identification of disease progression mechanisms for some mutations and have provided evidence to help explain genotype-phenotype correlations. However, many unanswered questions remain about the common and divergent pathological mechanisms that drive disease progression, and these mechanisms need to be understood in order to identify therapeutic targets. Several new transgenic animals have been described recently, expanding the spectrum of core myopathy models, including mice with patient-specific mutations. Furthermore, recent developments in 3D tissue engineering are expected to enable the study of core myopathy disease progression and the effects of potential therapeutic interventions in the context of human cells. In this Review, we summarize the current landscape of core myopathy models, and assess the hurdles and opportunities of future modeling strategies

Deep subcutaneous application of poly-L-lactic acid as a filler for facial lipoatrophy in HIV-infected patients

Introduction: Facial lipoatrophy is a crucial problem of HIV-infected patients undergoing highly active antiretroviral therapy (HAART). Poly-L-lactic acid (PLA), provided as New-Fill(R)/Sculptra(TM), is known as one possible treatment option. In 2004 PLA was approved by the FDA as Sculptra(TM) for the treatment of lipoatrophy of the face in HIV-infected patients. While the first trials demonstrated relevant efficacy, this was to some extent linked to unwanted effects. As the depth of injection was considered relevant in this context, the application modalities of the preparation were changed. The preparation was to be injected more deeply into subcutaneous tissue, after increased dilution. Material and Methods: To test this approach we performed a pilot study following the new recommendations in 14 patients. Results: While the efficacy turned out to be about the same, tolerability was markedly improved. The increase in facial dermal thickness was particularly obvious in those patients who had suffered from lipoatrophy for a comparatively small period of time. Conclusion: With the new recommendations to dilute PLA powder and to inject it into the deeper subcutaneous tissue nodule formation is a minor problem. However, good treatment results can only be achieved if lipoatrophy is not too intense; treatment intervals should be about 2 - 3 weeks. Copyright (C) 2005 S. Karger AG, Basel

Rethinking phylogeographic structure and historical refugia in the rufous-capped babbler Cyanoderma ruficeps in light of range-wide genetic sampling and paleodistributional reconstructions

Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderma ruficeps, and compare results to previous studies that examined this species across mainland China and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations (Nepal, Tibet, Myanmar, Yunnan), rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood

Correlating bacterial shedding with fecal corticosterone levels and serological responses from layer hens experimentally infected with Salmonella Typhimurium

Salmonella Enteriditis and Salmonella Typhimurium are commonly isolated during egg-related outbreaks of salmonellosis and represent a significant international public health issue. In Australia, Salmonella Typhimurium is the most common serovar identified in egg product related foodborne outbreaks. While a number of studies have investigated Salmonella shedding and host responses to infection, they have been conducted over a short time period. The present study sought to characterise bacterial shedding and host responses to infection in hens infected with only Salmonella Typhimurium or co-infected with both Salmonella Typhimurium and Salmonella Mbandaka over a 16 week period. Salmonella shedding was quantified using the most probable number and qPCR methods and was highly variable over the course of the experiment. On day 1, fecal corticosterone metabolites in birds infected with Salmonella Typhimurium (674.2 ± 109.3 pg/mg) were significantly higher than control (238.0 ± 12.62 pg/mg) or co-infected (175.4 ± 8.58 pg/mg) birds. The onset of lay occurred between weeks 6-8 post-infection (pi) and Fecal corticosterone metabolite (FCM) concentrations increased in both control and co-infected birds. Antibody responses to infection were monitored in both serum and yolk samples. Salmonella Typhimurium specific antibody was lower in co-infected animals than monoinfected animals. Bacterial loads in internal organs were characterised to determine persistence. Spleen, liver and caecal tonsils were positive for bacteria in both groups, indicating that Salmonella was not cleared from the birds and internal organ colonization could serve as a reservoir for continued bacterial shedding.Pardeep Sharma, Vivek V. Pande, Talia S. Moyle, Andrea R. McWhorter and Kapil K. Chousalka