Open access uptake in Germany 2010-2018: adoption in a diverse research landscape

This study investigates the development of open access (OA) to journal articles from authors affiliated with German universities and non-university research institutions in the period 2010-2018. Beyond determining the overall share of openly available articles, a systematic classification of distinct categories of OA publishing allowed us to identify different patterns of adoption of OA. Taking into account the particularities of the German research landscape, variations in terms of productivity, OA uptake and approaches to OA are examined at the meso-level and possible explanations are discussed. The development of the OA uptake is analysed for the different research sectors in Germany (universities, non-university research institutes of the Helmholtz Association, Fraunhofer Society, Max Planck Society, Leibniz Association, and government research agencies). Combining several data sources (incl. Web of Science, Unpaywall, an authority file of standardised German affiliation information, the ISSN-Gold-OA 3.0 list, and OpenDOAR), the study confirms the growth of the OA share mirroring the international trend reported in related studies. We found that 45% of all considered articles during the observed period were openly available at the time of analysis. Our findings show that subject-specific repositories are the most prevalent type of OA. However, the percentages for publication in fully OA journals and OA via institutional repositories show similarly steep increases. Enabling data-driven decision-making regarding the implementation of OA in Germany at the institutional level, the results of this study furthermore can serve as a baseline to assess the impact recent transformative agreements with major publishers will likely have on scholarly communication. Open Access uptake in Germany 2010-2018: Interactive Supplement: s. https://subugoe.github.io/oauni/articles/supplement.htm

Violating the splicing rules: TG dinucleotides function as alternative 3' splice sites in U2-dependent introns

TG dinucleotides functioning as alternative 3' splice sites were identified and experimentally verified in 36 human genes

Open Access –Towards a non-normative and systematic understanding

Taubert NC, Hobert A, Fraser N, Jahn N, Iravani E. Open Access –Towards a non-normative and systematic understanding. Submitted.The term Open Access not only describes a certain model of scholarly publishing – namely in digital format freely accessible to readers – but often also implies that free availability of research results is desirable, and hence has a normative character. Together with the large variety of presently used definitions of different Open Access types, this normativity hinders a systematic investigation of the development of open availability of scholarly literature. In this paper, we propose a non-normative definition of Open Access and its usage as a neutral, descriptive term in bibliometric studies and research on science. To this end, we first specify what normative figures are commonly associated with the term Open Access and then develop a neutral definition. We further identify distinguishing characteristics of openly accessible literature, called dimensions, and derive a classification scheme into Open Access categories based on these dimensions. Additionally, we present an operationalisation method to assign scientific publications to the respective categories in practice. Here, we describe useful data sources, which can be employed to gather the information needed for the classification of scholarly works according to the presented classification scheme

TassDB2 - A comprehensive database of subtle alternative splicing events

Background: Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species. \ud Description: We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay \ud (NMD) pathway. Links are provided to the UCSC genome browser and other external resources.\ud Conclusion: TassDB2, available via http://www.tassdb.info, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.\ud \ud doi: 10.1186/1471-2105-11-216\u

Human Impacts on Forest Biodiversity in Protected Walnut-Fruit Forests in Kyrgyzstan

We used a spatially explicit model of forest dynamics, supported by empirical field data and socioeconomic data, to examine the impacts of human disturbances on a protected forest landscape in Kyrgyzstan. Local use of 27 fruit and nut species was recorded and modeled. Results indicated that in the presence of fuelwood cutting with or without grazing, species of high socioeconomic impor- tance such as Juglans regia, Malus spp., and Armeniaca vulgaris were largely eliminated from the landscape after 50–150 yr. In the absence of disturbance or in the presence of grazing only, decline of these species occurred at a much lower rate, owing to competi- tive interactions between tree species. This suggests that the current intensity of fuelwood harvesting is not sustainable. Conversely, cur- rent grazing intensities were found to have relatively little impact on forest structure and composition, and could potentially play a positive role in supporting regeneration of tree species. These results indicate that both positive and negative impacts on biodiversity can arise from human populations living within a protected area. Potentially, these could be reconciled through the development of participatory approaches to conservation management within this reserve, to ensure the maintenance of its high conservation value while meeting human needs

Accurate prediction of NAGNAG alternative splicing

Alternative splicing (AS) involving NAGNAG tandem acceptors is an evolutionarily widespread class of AS. Recent predictions of alternative acceptor usage reported better results for acceptors separated by larger distances, than for NAGNAGs. To improve the latter, we aimed at the use of Bayesian networks (BN), and extensive experimental validation of the predictions. Using carefully constructed training and test datasets, a balanced sensitivity and specificity of ≥92% was achieved. A BN trained on the combined dataset was then used to make predictions, and 81% (38/47) of the experimentally tested predictions were verified. Using a BN learned on human data on six other genomes, we show that while the performance for the vertebrate genomes matches that achieved on human data, there is a slight drop for Drosophila and worm. Lastly, using the prediction accuracy according to experimental validation, we estimate the number of yet undiscovered alternative NAGNAGs. State of the art classifiers can produce highly accurate prediction of AS at NAGNAGs, indicating that we have identified the major features of the ‘NAGNAG-splicing code’ within the splice site and its immediate neighborhood. Our results suggest that the mechanism behind NAGNAG AS is simple, stochastic, and conserved among vertebrates and beyond

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape

Hobert A, Jahn N, Mayr P, Schmidt B, Taubert NC. Open Access Uptake in Germany 2010-18: Adoption in a diverse research landscape. Scientometrics. 2021.This study investigates the development of open access (OA) to journal articles from authors affiliated with German universities and non-university research institutions in the period 2010-2018. Beyond determining the overall share of openly available articles, a systematic classification of distinct categories of OA publishing allows to identify different patterns of adoption to OA. Taking into account the particularities of the German research landscape, variations in terms of productivity, OA uptake and approaches to OA are examined at the meso-level and possible explanations are discussed. The development of the OA uptake is analysed for the different research sectors in Germany (universities, non-university research institutes of the Helmholtz Association, Fraunhofer Society, Max Planck Society, Leibniz Association, and government research agencies). Combining several data sources (incl. Web of Science, Unpaywall, an authority file of standardised German affiliation information, the ISSN-Gold-OA 3.0 list, and OpenDOAR), the study confirms the growth of the OA share mirroring the international trend reported in related studies. We found that 45% of all considered articles in the observed period were openly available at the time of analysis. Our findings show that subject-specific repositories are the most prevalent OA type. However, the percentages for publication in fully OA journals and OA via institutional repositories show similarly steep increases. Enabling data-driven decision-making regarding OA implementation in Germany at the institutional level, the results of this study furthermore can serve as a baseline to assess the impact recent transformative agreements with major publishers will likely have on scholarly communication

Understanding differences of the OA uptake within the German university landscape (2010-2020) – Part 1: journal-based OA

Taubert NC, Hobert A, Jahn N, Bruns A, Iravani E. Understanding differences of the OA uptake within the German university landscape (2010-2020) – Part 1: journal-based OA. Submitted.This study investigates the determinants for the uptake of Full and Hybrid Open Access (OA) in the university landscape of Germany. It adapts the governance equaliser as a heuristic for this purpose and distinguishes between three factors: The disciplinary profile (academic self-governance), infrastructures and services of universities that aim to support OA (managerial self-governance) and large transformative agreements (part of state regulation). The uptake of OA, the influence of the disciplinary profile of universities and the influence of transformative agreements is measured by combining several data sources (incl. Web of Science, Unpaywall, an authority file of standardised German affiliation information, the ISSN-Gold-OA 4.0 list, and lists of publications covered by transformative agreements). For managerial self-governance, a structured data collection was created by harvesting different sources of information and by manual online search. To determine the explanatory power of the different factors, a series of regression analyses was performed for different periods and for both Full as well as Hybrid OA. As a result of the regression analyses, the most determining factor for the explanation of differences in the uptake of both OA-types turned out to be academic self-governance. For the year 2020, Hybrid OA transformative agreements have become a second relevant factor. However, all variables that reflect local infrastructural support and services for OA (managerial self-governance) turned out to be non-significant. To deepen the understanding of the adoption of OA on the level of institutions, the outcomes of the regression analyses are contextualised by an interview study conducted with 20 OA officers of German universities

Understanding differences of the OA uptake within the Germany university landscape (2010-2020) - Part 2: repository-provided OA

Taubert NC, Hobert A, Jahn N, Bruns A, Iravani E. Understanding differences of the OA uptake within the Germany university landscape (2010-2020) - Part 2: repository-provided OA. Submitted.This study investigates the determinants for the uptake of institutional and subject repository Open Access (OA) in the university landscape of Germany and considers three factors: The disciplinary profile of universities, their OA infrastructures and services and large transformative agreements. The uptake of OA as well as the determinants are measured by combining several data sources (incl. Web of Science, Unpaywall, an authority file of standardised German affiliation information, the ISSN-Gold-OA 4.0 list, and lists of publications covered by transformative agreements). For universities OA infrastructures and services, a structured data collection was created by harvesting different sources of information and by manual online search. To determine the explanatory power of the different factors, a series of regression analyses was performed for different periods and for both institutional as well as subject repository OA. As a result of the regression analyses, the most determining factor for the explanation of differences in the uptake of both repository OA-types turned out to be the disciplinary profile, whereas all variables that capture local infrastructural support and services for OA turned out to be non-significant. The outcome of the regression analyses is contextualised by an interview study conducted with 20 OA officers of German universities. The contextualisation provides hints that the original function of institutional repositories, offering a channel for secondary publishing is vanishing, while a new function of aggregation of metadata and full texts is becoming of increasing importance