Approaches to estimating the universe of natural history collections data

This contribution explores the problem of recognizing and measuring the universe of specimen-level data existing in Natural History Collections around the world, in absence of a complete, world-wide census or register. Estimates of size seem necessary to plan for resource allocation for digitization or data capture, and may help represent how many vouchered primary biodiversity data (in terms of collections, specimens or curatorial units) might remain to be mobilized. Three general approaches are proposed for further development, and initial estimates are given. Probabilistic models involve crossing data from a set of biodiversity datasets, finding commonalities and estimating the likelihood of totally obscure data from the fraction of known data missing from specific datasets in the set. Distribution models aim to find the underlying distribution of collections’ compositions, figuring out the occult sector of the distributions. Finally, case studies seek to compare digitized data from collections known to the world to the amount of data known to exist in the collection but not generally available or not digitized. Preliminary estimates range from 1.2 to 2.1 gigaunits, of which a mere 3% at most is currently web-accessible through GBIF’s mobilization efforts. However, further data and analyses, along with other approaches relying more heavily on surveys, might change the picture and possibly help narrow the estimate. In particular, unknown collections not having emerged through literature are the major source of uncertainty

Assessment of user needs of primary biodiversity data: Analysis, concerns, and challenges

A Content Needs Assessment (CNA) survey has been conducted in order to determine what GBIF-mediated data users may be using, what they would be using if available, and what they need in terms of primary biodiversity data records. The survey was launched in 2009 in six languages, and collected more than 700 individual responses. Analysis of the responses showed some lack of awareness about the availability of accessible primary data, and pointed out some types of data in high demand for linking to distribution and taxonomical data now derived from the GBIF cache. A notable example was linkages to molecular data. Also, the CNA survey uncovered some biases in the design of user needs surveys, by showing demographic and linguistic effects that may have influenced the distribution of responses received in analogous surveys conducted at the global scale

Validation of a rapid antigen test as a screening tool for SARS-CoV-2 infection in asymptomatic populations. Sensitivity, specificity and predictive values

Background: Early diagnosis of SARS-CoV-2 infection is essential to reduce disease spread. Rapid antigen tests have not been sufficiently evaluated in asymptomatic patients to be used as massive population screening tools. Methods: Head-to-head evaluation of Roche SARS-CoV-2 Rapid Antigen Test and real-time reverse transcription polymerase chain reaction (RT-PCR) as SARS-CoV-2 screening tools performed in asymptomatic adults from a semi-closed community in University of Navarra (Spain) from November 2020 to January 2021. Sensitivity, specificity and predictive values were calculated using RT-PCR as reference method. Findings: Roche SARS-CoV-2 Rapid Antigen Test was performed on 2542 asymptomatic adults in a community with a SARS-CoV-2 incidence of 1·93%. It showed a sensitivity of 71·43% (CI 95%: 56·74 – 83·42) and a specificity of 99·68% (CI 95%: 99·37 - 99·86). Positive Predictive Value was 81·4 (CI 95% 66·6 – 91·61) and Negative Predictive Value was 99·44 (CI 95% 99·06 – 99·69). Test sensitivity was related to viral load, with higher sensitivity in RT-PCR cycle threshold (Ct) values under 25 (93·75%, CI 95%: 71·96 – 98·93), that dropped to 29·41% (CI 95%: 10·31- 55·96) in RT-PCR Ct values above 25. Interpretation: This study suggests that rapid antigen tests are less effective in asymptomatic population, when compared with RT-PCR. Further studies are needed to evaluate different options to improve screenings based on rapid antigen test, such as the use of clinical questionnaires to select higher risk-participants, the confirmation of negative results with RT-PCR or the use of repetitive sequential testing

Content assessment of the primary biodiversity data published through GBIF network: Status, challenges and potentials

With the establishment of the Global Biodiversity Information Facility (GBIF) in 2001 as an inter-governmental co-ordinating body, concerted efforts were made during the past decade to establish a global research infrastructure to facilitate the sharing, discovery and access to primary biodiversity data. As on date the participants in GBIF have enabled the discovery and access to over 267+ million such data records. While this remarkable achievement in terms of volume of data must be acknowledged, concerns about the quality and ‘fitness-for-use’ of the data should also be carefully considered in future developments. This contribution is therefore a direct response to the calls for comprehensive content assessment of the GBIF mobilised data. It is the first comprehensive assessment of the coverage of the content mobilised so far through GBIF, as well as a mean to identify the existing gaps and reflect on fitness-for-use requirements. This paper describes the complementary methodologies adopted by the GBIF Secretariat and University of Navarra for the development of a comprehensive content assessment. Outcomes of these research initiatives are summarised in four categories, namely, (a) data quality assessment, (b) trends/patterns assessment, (c) fitness-for-use assessment, and (d) ecosystem specific data diversity assessment. In conclusion we make specific suggestions to the GBIF community on the adoption of common indicators to assess progress towards future targets as well as recommendations to populate such exercise at various levels within the GBIF Network from national level to thematic levels

Research applications of primary biodiversity databases in the digital age.

Our world is in the midst of unprecedented change-climate shifts and sustained, widespread habitat degradation have led to dramatic declines in biodiversity rivaling historical extinction events. At the same time, new approaches to publishing and integrating previously disconnected data resources promise to help provide the evidence needed for more efficient and effective conservation and management. Stakeholders have invested considerable resources to contribute to online databases of species occurrences. However, estimates suggest that only 10% of biocollections are available in digital form. The biocollections community must therefore continue to promote digitization efforts, which in part requires demonstrating compelling applications of the data. Our overarching goal is therefore to determine trends in use of mobilized species occurrence data since 2010, as online systems have grown and now provide over one billion records. To do this, we characterized 501 papers that use openly accessible biodiversity databases. Our standardized tagging protocol was based on key topics of interest, including: database(s) used, taxa addressed, general uses of data, other data types linked to species occurrence data, and data quality issues addressed. We found that the most common uses of online biodiversity databases have been to estimate species distribution and richness, to outline data compilation and publication, and to assist in developing species checklists or describing new species. Only 69% of papers in our dataset addressed one or more aspects of data quality, which is low considering common errors and biases known to exist in opportunistic datasets. Globally, we find that biodiversity databases are still in the initial stages of data compilation. Novel and integrative applications are restricted to certain taxonomic groups and regions with higher numbers of quality records. Continued data digitization, publication, enhancement, and quality control efforts are necessary to make biodiversity science more efficient and relevant in our fast-changing environment

Indirect biomass estimations in Collembola

We propose coefficients for regressions relating dry weight to body or tergite length in Folsomia candida, Entomobrya schoetti, Sminthurus viridis, and Hypogastrura vernalis (Collembola). Measurements were made on large batches of preserved, identified specimens. Batches were dessicated completely by critical-point drying and weighed. We compare our data with other published models and critically review the literature, finding questionable records

Reduction of exposure of cyclists to urban air pollution

This book collects the main outcomes that were generated during the implementation of the LIFE+RESPIRA project (LIFE13 ENV/ES/000417), carried out in the city of Pamplona, Navarra, Spain. The research was conducted by a cross-functional team made up of more than 30 researchers belonging to three entities: The University of Navarra, the Centre for Energy, Environmental and Technological Research (CIEMAT) and Environmental Management of Navarra (GAN-NIK)

Medidas para reducir la exposición de los ciclistas a los principales contaminantes atmosféricos urbanos

Recoge los principales resultados generados durante la realización del proyecto LIFE+RESPIRA, llevado a cabo en la ciudad de Pamplona (Navarra, España) por un equipo interdisciplinar constituido por más de 30 investigadores pertenecientes a la Universidad de Navarra, el Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT) y Gestión Ambiental de Navarra (GAN-NIK). El libro, que se ha publicado en castellano y en inglés, se ha dividido en 7 capítulos: 1. ¿Ciudades sostenibles? 2. Exposición de los ciudadanos a la contaminación atmosférica 3. Papel de la vegetación urbana en la calidad del aire 4. Modelos de alta resolución para evaluar la calidad del aire 5. Impactos de la contaminación urbana 6. Movilidad y sostenibilidad urbanas 7. Comunicación y educación ambiental. Este libro pretende ser una guía de utilidad para científicos, gestores y ciudadanos, aportando un conjunto de herramientas que permitan mejorar la calidad de vida de nuestras ciudades. Además, quiere rendir un homenaje a todos los voluntarios ciclistas que han participado en dicho proyecto y que son los verdaderos artífices del mismo, ya que gracias a su dedicación incondicional durante más de dos años, han proporcionado una cantidad ingente de datos sobre la calidad del aire de la ciudad de Pamplona