Open Access through the Depot

The mission of "the Depot" is to provide a service that enables all UK academics to share in the benefits of open access exposure for their post-print research outputs. It does this by providing a national intake and storage facility - the Depot - for use by any UK academic in Higher Education. This article describes the Depot and the service it provides.

Ceramics, Trade, Provenience and Geology: Cyprus in the Late Bronze Age

The island of Cyprus was a major producer of copper and stood at the heart of east Mediterranean trade networks during the Late Bronze Age. It may also have been the source of the Red Lustrous Wheelmade Ware that has been found in mortuary contexts in Egypt and the Levant, and in Hittite temple assemblages in Anatolia. Neutron Activation Analysis (NAA) has enabled the source area of this special ceramic to be located in a geologically highly localised and geochemically distinctive area of western Cyprus. This discovery offers a new perspective on the spatial organisation of Cypriot economies in the production and exchange of elite goods around the eastern Mediterranean at this time.

INTEGRATIVE BIOMARKER IDENTIFICATION AND CLASSIFICATION USING HIGH THROUGHPUT ASSAYS

It is well accepted that tumorigenesis is a multi-step procedure involving aberrant functioning of genes regulating cell proliferation, differentiation, apoptosis, genome stability, angiogenesis and motility. To obtain a full understanding of tumorigenesis, it is necessary to collect information on all aspects of cell activity. Recent advances in high throughput technologies allow biologists to generate massive amounts of data, more than might have been imagined decades ago. These advances have made it possible to launch comprehensive projects such as (TCGA) and (ICGC) which systematically characterize the molecular fingerprints of cancer cells using gene expression, methylation, copy number, microRNA and SNP microarrays as well as next generation sequencing assays interrogating somatic mutation, insertion, deletion, translocation and structural rearrangements. Given the massive amount of data, a major challenge is to integrate information from multiple sources and formulate testable hypotheses. This thesis focuses on developing methodologies for integrative analyses of genomic assays profiled on the same set of samples. We have developed several novel methods for integrative biomarker identification and cancer classification. We introduce a regression-based approach to identify biomarkers predictive to therapy response or survival by integrating multiple assays including gene expression, methylation and copy number data through penalized regression. To identify key cancer-specific genes accounting for multiple mechanisms of regulation, we have developed the integIRTy software that provides robust and reliable inferences about gene alteration by automatically adjusting for sample heterogeneity as well as technical artifacts using Item Response Theory. To cope with the increasing need for accurate cancer diagnosis and individualized therapy, we have developed a robust and powerful algorithm called SIBER to systematically identify bimodally expressed genes using next generation RNAseq data. We have shown that prediction models built from these bimodal genes have the same accuracy as models built from all genes. Further, prediction models with dichotomized gene expression measurements based on their bimodal shapes still perform well. The effectiveness of outcome prediction using discretized signals paves the road for more accurate and interpretable cancer classification by integrating signals from multiple sources.

Biodiversity survey of the UNESCO Sheka forest biosphere reserve from February 2016 to May 2016

Data of amphibians, reptiles and birds surveyed from February 2016 to May 2016 in the UNESCO Sheka forest biosphere reserve are provided as an online open access data file.

New species of Bakeriella (Hymenoptera, Bethylidae) from the New World and new data on geographic distribution

Bakeriella lata sp. nov. (Brazil, Rondônia), Bakeriella aurata sp. nov. (Brazil, Amazonas) and Bakeriella sulcaticeps sp. nov. (Brazil, Amazonas) are described and illustrated. New geographic records and variation data for B. cristata Evans, 1964, B. floridana Evans, 1964, B. flavicornis Kieffer, 1910, B. incompleta Azevedo, 1994, B. mira Evans, 1997, B. montivaga (Kieffer, 1910), B. olmeca Evans, 1964 and B. subcarinata Evans, 1965 are provided. The male of B. incompleta is described for the first time.

Cluster Analysis of Business Data

This journal provides immediate open access to its content on the principle that making research freely available to the public supports a greater global exchange of knowledge.

Clustering an interval data set : are the main partitions similar to a priori partition?

This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

OpenAIRE guidelines: supporting interoperability for Data Archives

OpenAIRE supports the European Commission Open Access policy by providing an infrastructure for researchers to comply with the European Union Open Access mandate. The current OpenAIRE infrastructure and services, resulting from OpenAIRE and OpenAIREplus FP7 projects, builds on Open Access research results from a wide range of repositories and other data sources: institutional or thematic publication repositories, Open Access journals, data repositories, Current Research Information Systems and aggregators. (...)

FOSTER: facilitate open science training for european research

FOSTER aims to support different stakeholders, especially young researchers, in adopting open access in the context of the European Research Area (ERA) and in complying with the open access policies and rules of participation set out for Horizon 2020 (H2020). FOSTER establish a European-wide training programme on open access and open data, consolidating training activities at downstream level and reaching diverse disciplinary communities and countries in the ERA. The training programme includes different approaches and delivery options: elearning, blearning, self-learning, dissemination of training materials/contents, helpdesk, face-to-face training, especially training-the-trainers, summer schools, seminars, etc.

An Ontology for Open Rubric Exchange on the Web

While the Internet has given educators access to a steady supply of Open Educational Resources, the educational rubrics commonly shared on the Web are generally in the form of static, non-semantic presentational documents or in the proprietary data structures of commercial content and learning management systems.With the advent of Semantic Web Standards, producers of online resources have a new framework to support the open exchange of software-readable datasets. Despite these advances, the state of the art of digital representation of rubrics as sharable documents has not progressed.This paper proposes an ontological model for digital rubrics. This model is built upon the Semantic Web Standards of the World Wide Web Consortium (W3C), principally the Resource Description Framework (RDF) and Web Ontology Language (OWL).

Epidemiological and clinical data of hospitalizations associated with respiratory syncytial virus infection in children under 5 years of age in Spain: FIVE multicenter study.

BACKGROUND Respiratory syncytial virus (RSV) is an important pathogen in lower respiratory tract infections (LRTI) in infants, but there are limited data concerning patients with underlying conditions and children older than 2 years of age. METHODS We have designed a prospective observational multicenter national study performed in 26 Spanish hospitals (December 2011-March 2012). Investigational cases were defined as children with underlying chronic diseases and were compared with a group of previously healthy children (proportion 1:2). Clinical data were compared between the groups. RESULTS A total of 1763 children hospitalized due to RSV infection during the inclusion period were analyzed. Of them, 225 cases and 460 healthy children were enrolled in the study. Underlying diseases observed were respiratory (64%), cardiovascular (25%), and neurologic (12%), as well as chromosomal abnormalities (7·5%), immunodeficiencies (6·7%), and inborn errors of metabolism (3·5%). Cases were statistically older than previously healthy children (average age: 16·3 versus 5·5 months). Cases experienced hypoxemia more frequently (P < 0·001), but patients with respiratory diseases required oxygen therapy more often (OR: 2·99; 95% CI: 1·03-8·65). Mechanical ventilation was used more in patients with cardiac diseases (OR: 3·0; 95% CI: 1·07-8·44) and in those with inborn errors of metabolism (OR: 12·27; 95% CI: 2·11-71·47). This subgroup showed a higher risk of admission to the PICU (OR: 6·7, 95% CI: 1·18-38·04). Diagnosis of pneumonia was more frequently found in cases (18·2% versus 9·3%; P < 0·01). CONCLUSIONS A significant percentage of children with RSV infection have underlying diseases and the illness severity is higher than in healthy children.

Measuring researchers' use of scholarly information through social bookmarking data: a case study of BibSonomy

This paper explores the possibility of using data from social bookmarking services to measure the use of information by academic researchers. Social bookmarking data can be used to augment participative methods (e.g. interviews and surveys) and other, non-participative methods (e.g. citation analysis and transaction logs) to measure the use of scholarly information. We use BibSonomy, a free resource-sharing system, as a case study. Results show that published journal articles are by far the most popular type of source bookmarked, followed by conference proceedings and books. Commercial journal publisher platforms are the most popular type of information resource bookmarked, followed by websites, records in databases and digital repositories. Usage of open access information resources is low in comparison with toll access journals. In the case of open access repositories, there is a marked preference for the use of subject-based repositories over institutional repositories. The results are consistent with those observed in related studies based on surveys and citation analysis, confirming the possible use of bookmarking data in studies of information behaviour in academic settings. The main advantages of using social bookmarking data are that is an unobtrusive approach, it captures the reading habits of researchers who are not necessarily authors, and data are readily available. The main limitation is that a significant amount of human resources is required in cleaning and standardizing the data.

Reliable selfing rate estimates from imperfect population genetic data.

Genotypic frequencies at codominant marker loci in population samples convey information on mating systems. A classical way to extract this information is to measure heterozygote deficiencies (FIS) and obtain the selfing rate s from FIS = s/(2 - s), assuming inbreeding equilibrium. A major drawback is that heterozygote deficiencies are often present without selfing, owing largely to technical artefacts such as null alleles or partial dominance. We show here that, in the absence of gametic disequilibrium, the multilocus structure can be used to derive estimates of s independent of FIS and free of technical biases. Their statistical power and precision are comparable to those of FIS, although they are sensitive to certain types of gametic disequilibria, a bias shared with progeny-array methods but not FIS. We analyse four real data sets spanning a range of mating systems. In two examples, we obtain s = 0 despite positive FIS, strongly suggesting that the latter are artefactual. In the remaining examples, all estimates are consistent. All the computations have been implemented in a open-access and user-friendly software called rmes (robust multilocus estimate of selfing) available at http://ftp.cefe.cnrs.fr, and can be used on any multilocus data. Being able to extract the reliable information from imperfect data, our method opens the way to make use of the ever-growing number of published population genetic studies, in addition to the more demanding progeny-array approaches, to investigate selfing rates.

The Case for Linking World Law Data

The present paper advocates for the creation of a federated, hybrid database in the cloud, integrating law data from all available public sources in one single open access system - adding, in the process, relevant meta-data to the indexed documents, including the identification of social and semantic entities and the relationships between them, using linked open data techniques and standards such as RDF. Examples of potential benefits and applications of this approach are also provided, including, among others, experiences from of our previous research, in which data integration, graph databases and social and semantic networks analysis were used to identify power relations, litigation dynamics and cross-references patterns both intra and inter-institutionally, covering most of the World international economic courts.