Taxonbridge: an R package to create custom taxonomies based on the NCBI and GBIF taxonomies

Biological taxonomies establish conventions by which researchers can catalogue and systematically compare their work using nomenclature such as species binomial names and reference identifiers. The ideal taxonomy is unambiguous and exhaustive; however, no such single taxonomy exists, partly due to continuous changes and contributions made to existing taxonomies. The degree to which a taxonomy is useful furthermore depends on context provided by such variables as the taxonomic neighbourhood of a species (e.g., selecting arthropod or vertebrate species) or the geological time frame of the study (e.g., selecting extinct versus extant species). Collating the most relevant taxonomic information from multiple taxonomies is hampered by arbitrarily defined identifiers, ambiguity in scientific names, as well as duplicated and erroneous entries. The goal of taxonbridge is to provide tools for merging the Global Biodiversity Information Facility (GBIF) Backbone Taxonomy and the United States National Center for Biotechnology Information (NCBI) Taxonomy in order to create consistent, deduplicated and disambiguated custom taxonomies that reference both extant and extinct species

Multisite campaign on the open cluster M67. III. Delta Scuti pulsations in the blue stragglers

We have made an asteroseismic analysis of the variable blue stragglers in the open cluster M67. The data set consists of photometric time series from eight sites using nine 0.6-2.1 meter telescopes with a time baseline of 43 days. In two stars, EW Cnc and EX Cnc, we detect the highest number of frequencies (41 and 26) detected in delta Scuti stars belonging to a stellar cluster, and EW Cnc has the second highest number of frequencies detected in any delta Scuti star. We have computed a grid of pulsation models that take the effects of rotation into account. The distribution of observed and theoretical frequencies show that in a wide frequency range a significant fraction of the radial and non-radial low-degree modes are excited to detectable amplitudes. Despite the large number of observed frequencies we cannot constrain the fundamental parameters of the stars. To make progress we need to identify the degrees of some of the modes either from multi-colour photometry or spectroscopy.Comment: 15 pages, 14 figs, one appendix. Part three in a series of papers describing results from an extensive multi-site campaign on the open cluster M6

Multi-site campaign on the open cluster M67. I. Observations and photometric reductions

We report on an ambitious multi-site campaign aimed at detecting stellar variability, particularly solar-like oscillations, in the red giant stars in the open cluster M67 (NGC 2682). During the six-week observing run, which comprised 164 telescope nights, we used nine 0.6-m to 2.1-m class telescopes located around the world to obtain uninterrupted time-series photometry. We outline here the data acquisition and reduction, with emphasis on the optimisation of the signal-to-noise of the low amplitude (50-500 micromag) solar-like oscillations. This includes a new and efficient method for obtaining the linearity profile of the CCD response at ultra high precision (~10 parts per million). The noise in the final time series is 0.50 mmag per minute integration for the best site, while the noise in the Fourier spectrum of all sites combined is 20 micromag. In addition to the red giant stars, this data set proves to be very valuable for studying high-amplitude variable stars such as eclipsing binaries, W UMa systems and delta Scuti stars.Comment: 12 pages, 13 figures, accepted by MNRA

Looking back, looking forward: Methodological challenges and future directions in research on persons with profound intellectual and multiple disabilities

Within the context of the Special Interest Research Group (SIRG) on Persons with Profound Intellectual and Multiple Disabilities (PIMD), researchers often discuss the methodological problems and challenges they are confronted with. The aim of the current article was to give an overview of these challenges. The challenges are centred on six topics. These reflect the main components of a study's design: (a) participant demarcation, (b) participant recruitment, (c) data collection and instruments, (d) data analysis, (e) ethics/including the “voice” of persons with PIMD and (f) theoretical models. Next, to describing the specific challenges, possible solutions and pathways to address them are discussed. These are illustrated by recent studies by the authors and other researchers in the field. The current contribution wants to stimulate further discussion and ex-change of ideas, and the development of creative research techniques

European soybean to benefit people and the environment.

Europe imports large amounts of soybean that are predominantly used for livestock feed, mainly sourced from Brazil, USA and Argentina. In addition, the demand for GM-free soybean for human consumption is project to increase. Soybean has higher protein quality and digestibility than other legumes, along with high concentrations of isoflavones, phytosterols and minerals that enhance the nutritional value as a human food ingredient. Here, we examine the potential to increase soybean production across Europe for livestock feed and direct human consumption, and review possible effects on the environment and human health. Simulations and field data indicate rainfed soybean yields of 3.1 ± 1.2 t ha-1 from southern UK through to southern Europe (compared to a 3.5 t ha-1 average from North America). Drought-prone southern regions and cooler northern regions require breeding to incorporate stress-tolerance traits. Literature synthesized in this work evidenced soybean properties important to human nutrition, health, and traits related to food processing compared to alternative protein sources. While acknowledging the uncertainties inherent in any modelling exercise, our findings suggest that further integrating soybean into European agriculture could reduce GHG emissions by 37-291 Mt CO2e year-1 and fertiliser N use by 0.6-1.2 Mt year-1, concurrently improving human health and nutrition

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio