Recommendations for the Visibility of Open Access Publications in the Search Engine of the Austrian Library Network: Report of the OBV Working Group “Repositories in the Network”

Im vorliegenden Beitrag werden die Ergebnisse der OBV-Arbeitsgruppe „Repositorien im Verbund“ präsentiert. Die AG verfolgte das Ziel, einen Leitfaden für die Erfassung von Metadaten für Objekte in Repositorien, der dazu beiträgt, einheitliche Standards in dieser Hinsicht zu entwickeln, mit dessen Hilfe es in weiterer Folge ermöglicht werden soll, Repositorienbestände ohne Erzeugung von Dubletten in Alma bzw. im Verbundkatalog nachzuweisen. Weitere Ziele waren die Erarbeitung von Empfehlungen für eine zentrale Bereitstellung von Metadaten von Open Access-Publikationen zur Vereinfachung der lokalen Workflows (analog zum DFG-geförderten Projekt DeepGreen) mittels Teilautomatisierung sowie von Empfehlungen für eine Etablierung eines Reiters für Open Access-Materialien in der Suchmaschine des Österreichischen Bibliothekenverbundes (analog zu den Reitern „Fachliteratur“, „Hochschulschriften“ und „Nachlässe / Handschriften“).This paper presents the results of the OBV working group “Repositories in the Austrian Library Network”. The aim of the working group was to develop a guideline for the registration of metadata for objects in repositories, which would contribute to the development of uniform standards in this regard, and with the help of which it should subsequently be possible to identify repository holdings in Alma or in the Austrian Union Catalogue without creating duplicates. Further goals were the development of recommendations for a central provision of metadata of open access publications to simplify local workflows (analogous to the DFG-funded project DeepGreen) by means of partial automation, as well as recommendations for establishing a tab for open access materials in the search engine of the Austrian Library Network (analogous to the tabs “Literature”, “Theses and Dissertations” and “Bequests / Autographs”)

Digital sequence information is changing the way genetic resources are used in agricultural research and development: implications for new benefit-sharing norms

This paper analyses the ways in which CGIAR Centers use digital sequence information (DSI) in their efforts to conserve and sustainably utilize the world’s most important crop and livestock genetic diversity. The paper then reflects on which of the benefit-sharing options currently under consideration by the Contracting Parties to the CBD (and the versions of those options that must be considered by the Governing Body of the Plant Treaty and the UN FAO Commission on Genetic Resources for Food and Agriculture) would provide effective policy support for the continued use of DSI in agricultural research and development in the future

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Meningitis and epididymitis caused by Toscana virus infection imported to Switzerland diagnosed by metagenomic sequencing: a case report

BACKGROUND We report a rare case of Toscana virus infection imported into Switzerland in a 23-year old man who travelled to Imperia (Italy) 10 days before onset of symptoms. Symptoms included both meningitis and as well epididymitis. This is only the fourth case of Toscana virus reported in Switzerland. CASE PRESENTATION The patient presented with lymphocytic meningitis and scrotal pain due to epididymitis. Meningitis was initially treated with ceftriaxone. Herpes simplex, tick-borne encephalitis, enterovirus, measles, mumps, rubella and Treponema pallidum were excluded with specific polymerase chain reaction (PCR) or serology. In support of routine diagnostic PCR and serology assays, unbiased viral metagenomic sequencing was performed of cerebrospinal fluid and serum. Toscana virus infection was identified in cerebrospinal fluid and the full coding sequence could be obtained. Specific PCR in cerebrospinal fluid and blood and serology with Immunoglobulin (Ig) M and IgG against Toscana virus confirmed our diagnosis. Neurological symptoms recovered spontaneously after 5 days. CONCLUSIONS This case of Toscana virus infection highlights the benefits of unbiased metagenomic sequencing to support routine diagnostics in rare or unexpected viral infections. With increasing travel histories of patients, physicians should be aware of imported Toscana virus as the agent for viral meningitis and meningoencephalitis

Genotypic Prediction of Co-receptor Tropism of HIV-1 Subtypes A and C

Antiretroviral treatment of Human Immunodeficiency Virus type-1 (HIV-1) infections with CCR5-antagonists requires the co-receptor usage prediction of viral strains. Currently available tools are mostly designed based on subtype B strains and thus are in general not applicable to non-B subtypes. However, HIV-1 infections caused by subtype B only account for approximately 11% of infections worldwide. We evaluated the performance of several sequence-based algorithms for co-receptor usage prediction employed on subtype A V3 sequences including circulating recombinant forms (CRFs) and subtype C strains. We further analysed sequence profiles of gp120 regions of subtype A, B and C to explore functional relationships to entry phenotypes. Our analyses clearly demonstrate that state-of- the-art algorithms are not useful for predicting co-receptor tropism of subtype A and its CRFs. Sequence profile analysis of gp120 revealed molecular variability in subtype A viruses. Especially, the V2 loop region could be associated with co-receptor tropism, which might indicate a unique pattern that determines co-receptor tropism in subtype A strains compared to subtype B and C strains. Thus, our study demonstrates that there is a need for the development of novel algorithms facilitating tropism prediction of HIV-1 subtype A to improve effective antiretroviral treatment in patients

Ecotypic differentiation under farmers' selection: Molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes

La comprensión de la distribución de la diversidad genética de los cultivos en relación con los factores ambientales puede dar una idea de los procesos eco-evolutivos involucrados en la domesticación de las plantas. La jícama (Pachyrhizus Rich. ex DC.) es un conjunto de leguminosas cultivadas nativas de América del Sur y Central que se cultivan por sus raíces tuberosas pero son propagadas por semillas. Utilizando un enfoque genético de paisaje, examinamos las correlaciones entre los factores ambientales y los patrones filogeográficos de diversidad genética en las poblaciones de Pachyrhizus landrace. Los análisis moleculares basados en la secuenciación del ADN del cloroplasto y un nuevo conjunto de marcadores de microsatélites nucleares revelaron dos linajes distintos, con una fuerte diferenciación genética entre las razas locales andinas (linaje A) y las amazónicas (linaje B). La comparación de diferentes escenarios evolutivos para la historia de la diversificación del ñame en los Andes utilizando cálculos bayesianos aproximados sugiere que Pachyrhizus ahipa y Pachyrhizus tuberosus comparten una relación progenitora derivada, con factores ambientales que juegan un papel importante en la selección de ecotipos divergentes. Los nuevos datos moleculares requieren una revisión de la taxonomía de Pachyrhizus pero son congruentes con la evidencia paleoclimática y arqueológica, y sugieren que la selección para un crecimiento determinado fue parte de las adaptaciones ecofisiológicas asociadas con la diversificación del complejo P. tuberosus y P. ahipa durante el Holoceno medio.Revisado por pare

Data from: Ecotypic differentiation under farmers’ selection: molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes

Understanding the distribution of crop genetic diversity in relation to environmental factors can give insights into the eco-evolutionary processes involved in plant domestication. Yam beans (Pachyrhizus Rich. ex DC.) are leguminous crops native to South and Central America that are grown for their tuberous roots but are seed-propagated. Using a landscape genetic approach, we examined correlations between environmental factors and phylogeographic patterns of genetic diversity in Pachyrhizus landrace populations. Molecular analyses based on chloroplast DNA sequencing and a new set of nuclear microsatellite markers revealed two distinct lineages, with strong genetic differentiation between Andean landraces (lineage A) and Amazonian landraces (lineage B). The comparison of different evolutionary scenarios for the diversification history of yam beans in the Andes using Approximate Bayesian Computation (ABC) suggests that P. ahipa and P. tuberosus share a progenitor-derivative relationship, with environmental factors playing an important role in driving selection for divergent ecotypes. The new molecular data call for a revision of the taxonomy of Pachyrhizus but are congruent with palaeoclimatic and archaeological evidence, and suggest that selection for determinate growth was part of ecophysiological adaptations associated with the diversification of the P. tuberosus–P. ahipa complex during the Mid-Holocene

Data from: Ecotypic differentiation under farmers’ selection: molecular insights into the domestication of Pachyrhizus Rich. ex DC. (Fabaceae) in the Peruvian Andes

Understanding the distribution of crop genetic diversity in relation to environmental factors can give insights into the eco-evolutionary processes involved in plant domestication. Yam beans (Pachyrhizus Rich. ex DC.) are leguminous crops native to South and Central America that are grown for their tuberous roots but are seed-propagated. Using a landscape genetic approach, we examined correlations between environmental factors and phylogeographic patterns of genetic diversity in Pachyrhizus landrace populations. Molecular analyses based on chloroplast DNA sequencing and a new set of nuclear microsatellite markers revealed two distinct lineages, with strong genetic differentiation between Andean landraces (lineage A) and Amazonian landraces (lineage B). The comparison of different evolutionary scenarios for the diversification history of yam beans in the Andes using Approximate Bayesian Computation (ABC) suggests that P. ahipa and P. tuberosus share a progenitor-derivative relationship, with environmental factors playing an important role in driving selection for divergent ecotypes. The new molecular data call for a revision of the taxonomy of Pachyrhizus but are congruent with palaeoclimatic and archaeological evidence, and suggest that selection for determinate growth was part of ecophysiological adaptations associated with the diversification of the P. tuberosus–P. ahipa complex during the Mid-Holocene