Linked Data Publication of Live Music Archives and Analyses

date-added: 2017-12-22 15:39:21 +0000 date-modified: 2017-12-22 15:53:18 +0000 keywords: Linked Data, Semantic Audio, Semantic Web, live music archive local-url: https://link.springer.com/chapter/10.1007/978-3-319-68204-4_3 bdsk-url-1: https://iswc2017.semanticweb.org/wp-content/uploads/papers/MainProceedings/221.pdf bdsk-url-2: https://dx.doi.org/10.1007/978-3-319-68204-4_3date-added: 2017-12-22 15:39:21 +0000 date-modified: 2017-12-22 15:53:18 +0000 keywords: Linked Data, Semantic Audio, Semantic Web, live music archive local-url: https://link.springer.com/chapter/10.1007/978-3-319-68204-4_3 bdsk-url-1: https://iswc2017.semanticweb.org/wp-content/uploads/papers/MainProceedings/221.pdf bdsk-url-2: https://dx.doi.org/10.1007/978-3-319-68204-4_3We describe the publication of a linked data set exposing metadata from the Internet Archive Live Music Archive along with detailed feature analysis data of the audio files contained in the archive. The collection is linked to existing musical and geographical resources allowing for the extraction of useful or nteresting subsets of data using additional metadata. The collection is published using a ‘layered’ approach, aggregating the original information with links and specialised analyses, and forms a valuable resource for those investigating or developing audio analysis tools and workflows

Knowledge Driven Intelligent Survey Systems for Linguists

This work was supported the EU Marie Curie K-Drive project (286348).Postprin

Informatics Technology Mimics Ecology: Dense, Mutualistic Collaboration Networks Are Associated with Higher Publication Rates

Information technology (IT) adoption enables biomedical research. Publications are an accepted measure of research output, and network models can describe the collaborative nature of publication. In particular, ecological networks can serve as analogies for publication and technology adoption. We constructed network models of adoption of bioinformatics programming languages and health IT (HIT) from the literature

A Digital Repository and Execution Platform for Interactive Scholarly Publications in Neuroscience

The CARMEN Virtual Laboratory (VL) is a cloud-based platform which allows neuroscientists to store, share, develop, execute, reproduce and publicise their work. This paper describes new functionality in the CARMEN VL: an interactive publications repository. This new facility allows users to link data and software to publications. This enables other users to examine data and software associated with the publication and execute the associated software within the VL using the same data as the authors used in the publication. The cloud-based architecture and SaaS (Software as a Service) framework allows vast data sets to be uploaded and analysed using software services. Thus, this new interactive publications facility allows others to build on research results through reuse. This aligns with recent developments by funding agencies, institutions, and publishers with a move to open access research. Open access provides reproducibility and verification of research resources and results. Publications and their associated data and software will be assured of long-term preservation and curation in the repository. Further, analysing research data and the evaluations described in publications frequently requires a number of execution stages many of which are iterative. The VL provides a scientific workflow environment to combine software services into a processing tree. These workflows can also be associated with publications and executed by users. The VL also provides a secure environment where users can decide the access rights for each resource to ensure copyright and privacy restrictions are met

Three Essential Ribonucleases—RNase Y, J1, and III—Control the Abundance of a Majority of Bacillus subtilis mRNAs

Bacillus subtilis possesses three essential enzymes thought to be involved in mRNA decay to varying degrees, namely RNase Y, RNase J1, and RNase III. Using recently developed high-resolution tiling arrays, we examined the effect of depletion of each of these enzymes on RNA abundance over the whole genome. The data are consistent with a model in which the degradation of a significant number of transcripts is dependent on endonucleolytic cleavage by RNase Y, followed by degradation of the downstream fragment by the 5′–3′ exoribonuclease RNase J1. However, many full-size transcripts also accumulate under conditions of RNase J1 insufficiency, compatible with a model whereby RNase J1 degrades transcripts either directly from the 5′ end or very close to it. Although the abundance of a large number of transcripts was altered by depletion of RNase III, this appears to result primarily from indirect transcriptional effects. Lastly, RNase depletion led to the stabilization of many low-abundance potential regulatory RNAs, both in intergenic regions and in the antisense orientation to known transcripts

Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression

RNA turnover plays an important role in both virulence and adaptation to stress in the Gram-positive human pathogen Staphylococcus aureus. However, the molecular players and mechanisms involved in these processes are poorly understood. Here, we explored the functions of S. aureus endoribonuclease III (RNase III), a member of the ubiquitous family of double-strand-specific endoribonucleases. To define genomic transcripts that are bound and processed by RNase III, we performed deep sequencing on cDNA libraries generated from RNAs that were co-immunoprecipitated with wild-type RNase III or two different cleavage-defective mutant variants in vivo. Several newly identified RNase III targets were validated by independent experimental methods. We identified various classes of structured RNAs as RNase III substrates and demonstrated that this enzyme is involved in the maturation of rRNAs and tRNAs, regulates the turnover of mRNAs and non-coding RNAs, and autoregulates its synthesis by cleaving within the coding region of its own mRNA. Moreover, we identified a positive effect of RNase III on protein synthesis based on novel mechanisms. RNase III–mediated cleavage in the 5′ untranslated region (5′UTR) enhanced the stability and translation of cspA mRNA, which encodes the major cold-shock protein. Furthermore, RNase III cleaved overlapping 5′UTRs of divergently transcribed genes to generate leaderless mRNAs, which constitutes a novel way to co-regulate neighboring genes. In agreement with recent findings, low abundance antisense RNAs covering 44% of the annotated genes were captured by co-immunoprecipitation with RNase III mutant proteins. Thus, in addition to gene regulation, RNase III is associated with RNA quality control of pervasive transcription. Overall, this study illustrates the complexity of post-transcriptional regulation mediated by RNase III

Learning to live together: mutualism between self-splicing introns and their hosts

Group I and II introns can be considered as molecular parasites that interrupt protein-coding and structural RNA genes in all domains of life. They function as self-splicing ribozymes and thereby limit the phenotypic costs associated with disruption of a host gene while they act as mobile DNA elements to promote their spread within and between genomes. Once considered purely selfish DNA elements, they now seem, in the light of recent work on the molecular mechanisms regulating bacterial and phage group I and II intron dynamics, to show evidence of co-evolution with their hosts. These previously underappreciated relationships serve the co-evolving entities particularly well in times of environmental stress

A Review of occupation-based social classifications for social survey research

This article is a review of issues associated with measuring occupations and using occupation-based socio-economic classifications in social science research. The review is orientated towards researchers who undertake secondary analysis of large-scale micro-level social science datasets. This article begins with an outline of how to handle raw occupational information. This is followed by an introduction to the two main approaches to measuring occupations and a third lesser known but intellectually innovative approach. The three approaches are social class schemes, social stratification scales and the microclass approach. International comparisons are briefly described and a discussion of intersectionality with other key variables such as age and gender is provided. We are careful to emphasise that this article does not advocate the uncritical adoption of any one particular occupation-based socio-economic measure over and above other alternatives. Rather, we are advocating that researchers should choose from the portfolio of existing socio-economic measures in an informed and empirically defensible way, and we strongly advocate undertaking sensitivity analyses. We conclude that researchers should always use existing socio-economic measures that have agreed on and well-documented standards. We strongly advise researchers not to develop their own measures without strong justification nor to use existing measures in an un-prescribed or ad hoc manner