Envisaging a global infrastructure to exploit the potential of digitised collections.

Tens of millions of images from biological collections have become available online over the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. While image analysis has become mainstream in consumer applications, it is still used only on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if images of collection objects could be made accessible in a single corpus. In this paper, we make the case for infrastructure that could support image analysis of collection objects. We show that such infrastructure is entirely feasible and well worth investing in.

Association between COVID-19 and outstanding academic performance at a Spanish university.

BACKGROUND: SARS-CoV-2 is the causative agent of COVID-19 identified in December 2019, an acute infectious respiratory disease that can cause persistent neurological and musculoskeletal symptoms such as headache, fatigue, myalgias difficulty concentrating, among others including acute cerebrovascular disease with a prevalence of 1-35%. The aim of this study is to evaluate the impact of COVID-19 in undergraduate students on their academic performance as an indicator of their intellectual ability and performance in a university that maintained 100% face-to-face teaching during the 2020-2021 academic year. METHODS: A total of 7,039 undergraduate students were analyzed in a prospective cohort study at the University of Navarra. A questionnaire including sociodemographic and behavioral questions was sent. PCRs were performed throughout the academic year for the diagnosis of SARS-CoV-2 infection and students' academic results were provided by the academic center, adjusted descriptive and multivariate models were performed to assess the association. RESULTS: A total of 658 (9.3%) participants were diagnosed with COVID-19, almost 4.0% of them achieved outstanding academic results, while uninfected students did so in 7.3%. SARS-CoV-2 infection was associated with a significant decrease in having outstanding academic results (OR = 0.57; 95% CI: 0.38-0.86). CONCLUSION: Having COVID-19 disease, decreased academic performance in undergraduate students. Therefore, it is necessary to prevent infection even in the youngest sections of the population.

Behavioral and Personal Characteristics Associated With Risk of SARS-CoV-2 Infection in a Spanish University Cohort.

The aim of this study was to analyze the life habits and personal factors associated with increased severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) risk in a university environment with in-person lectures during the coronavirus disease 2019 (COVID-19) pandemic. To our knowledge, there are no previous longitudinal studies that have analyzed associations of behavioral and personal factors with the risk of SARS-CoV-2 infection on an entire university population. A cohort study was conducted in the 3 campuses of the University of Navarra between August 24, 2020, and May 30, 2021, including 14,496 students and employees; the final sample included 10,959. Descriptive and multivariate-adjusted models were fitted using Cox regression. A total of 1,032 (9.4%) participants were diagnosed with COVID-19 (879 students and 153 employees), almost 50% living with their families. COVID-19 was associated with living in college or residence (hazard ratio (HR) = 1.96, 95% CI: 1.45, 2.64), motor transportation (HR = 1.35, 95% CI: 1.14, 1.61), South American origin (HR = 1.43, 95% CI: 1.20, 1.72), and belonging to Madrid's campus (HR = 3.11, 95% CI: 2.47, 3.92). International students, especially from Latin America, mostly lived in university apartments or shared flats and cohabited with 4-11 people. Living in a big city (Madrid), was a significant risk factor.

Crosscutting of the pollutants and building ventilation systems: a literature review.

Considering the time spent in enclosed environments, it is essential to study the relationship between pollutants and building ventilation systems to find whether the types and levels of pollutants and greenhouse gasses, which are expected to be exhaled through ventilation systems into the atmosphere, have been adequately evaluated. We propose the hypothesis that the exhaled air from residential buildings contains pollutants that may become another source of contamination affecting urban air quality and potentially contributing to climate drivers. Thus, the main goal of this article is to present a cross-review of the identification of pollutants expected to be exhaled through ventilation systems in residential buildings. This approach has created the concept of "exhalation of buildings" a new concept enclosed within the research project in which this article is included. We analyze the studies related to the most significant pollutants found in buildings and the studies about the relation of buildings' ventilation systems with such pollutants. Our results show that, on the one hand, the increase in the use of mechanical ventilation systems in residential buildings has been demonstrated to enhance the ventilation rate and generally improve the indoor air quality conditions. But no knowledge could be extracted about the corresponding environmental cost of this improvement, as no systematic data were found about the total mass of contaminants exhaled by those ventilation systems. At the same time, no projects were found that showed a quantitative study on exhalation from buildings, contrary to the existence of studies on pollutants in indoor air.

Alternaria spore exposure in Bavaria, Germany, measured using artificial intelligence algorithms in a network of BAA500 automatic pollen monitors.

Although Alternaria spores are well-known allergenic fungal spores, automatic bioaerosol recognition systems have not been trained to recognize these particles until now. Here we report the development of a new algorithm able to classify Alternaria spores with BAA500 automatic bioaerosol monitors. The best validation score was obtained when the model was trained on both data from the original dataset and artificially generated images, with a validation unweighted mean Intersection over Union (IoU), also called Jaccard Index, of 0.95. Data augmentation techniques were applied to the training set. While some particles were not recognized (false negatives), false positives were few. The results correlated well with manual counts (mean of four Hirst-type traps), with R2 = 0.78. Counts from BAA500 were 1.92 times lower than with Hirst-type traps. The algorithm was then used to re-analyze the historical automatic pollen monitoring network (ePIN) dataset (2018-2022), which lacked Alternaria spore counts. Re-analysis of past data showed that Alternaria spore exposure in Bavaria was very variable, with the highest counts in the North (Marktheidenfeld, 154 m a.s.l.), and the lowest values close to the mountains in the South (Garmisch-Partenkirchen, 735 m a.s.l.). This approach shows that in our network future algorithms can be run on past datasets. Over time, the use of different algorithms could lead to misinterpretations as stemming from climate change or other phenological causes. Our approach enables consistent, homogeneous treatment of long-term series, thus preventing variability in particle counts owing to changes in the algorithms.

Control of SARS-CoV-2 Infection Rates at a Spanish University With In-Person Class Attendance.

The "Safe Campus Program," implemented in 2020 through 2021 at the University of Navarra (Spain), aimed to guarantee a safe return to university campus and prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks, avoiding university-wide lockdown. It included COVID-19 education, campus adaptation, and polymerase chain reaction (PCR) testing. We describe the main characteristics of the program and analyze the SARS-CoV-2 cumulative incidence among 14 496 university members. The 14-day cumulative incidence in the university was 415.2 versus 447.7 in the region. The program, sustainable in the long term, achieved low SARS-CoV-2 in-campus rates. (Am J Public Health. 2022;112(4):570-573. https://doi.org/10.2105/AJPH.2021.306682.

Environmental drivers of the seasonal exposure to airborne Alternaria spores in Spain.

Alternaria conidia have high allergenic potential and they can trigger important respiratory diseases. Due to that and to their extensive detection period, airborne Alternaria spores are considered as a relevant airborne allergenic particle. Several studies have been developed in order to predict the human exposure to this aeroallergen and to prevent their negative effects on sensitive population. These studies revealed that some sampling locations usually have just one single Alternaria spore season while other locations generally have two seasons within the same year. However, the reasons of these two different seasonal patterns remain unclear. To understand them better, the present study was carried out in order to determine if there are any weather conditions that influence these different behaviours at different sampling locations. With this purpose, the airborne Alternaria spore concentrations of 18 sampling locations in a wide range of latitudinal, altitudinal and climate ranges of Spain were studied. The aerobiological samples were obtained by means of Hirst-Type volumetric pollen traps, and the seasonality of the airborne Alternaria spores were analysed. The optimal weather conditions for spore production were studied, and the main weather factor affecting Alternaria spore seasonality were analysed by means of random forests and regression trees. The results showed that the temperature was the most relevant variable for the Alternaria spore dispersion and it influenced both the spore integrals and their seasonality. The water availability was also a very significant variable. Warmer sampling locations generally have a longer period of Alternaria spore detection. However, the spore production declines during the summer when the temperatures are extremely warm, what splits the favourable period for Alternaria spore production and dispersion into two separate ones, detected as two Alternaria spore seasons within the same year.

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. FUNDING: This research received no external funding.

Global trends in research output by zoos and aquariums.

Zoos and aquaria, often regarded as preservation-cum-entertainment enterprises, are also actors in the effort to curb the biodiversity crisis: raising awareness, supporting conservation, and conducting research. We assessed trends in zoo and aquaria research topics and study organisms over time worldwide. For the zoos and aquaria registered in the Species360's Zoological Information Management System and the World Association of Zoos and Aquariums, we compiled metadata on their research published in the peer-reviewed literature indexed in Scopus and carried out a keyword frequency analysis. The production of scientific papers by zoos increased at a much faster rate than the average accrual of scientific papers in the literature. Evolution of research themes ran parallel to that of biological sciences (e.g., development of molecular genetics or increased awareness about conservation). The focus of 48.5% of zoo-led research was on vertebrates, of which mammal research was 33.7%. Whether zoos are effectively contributing to conservation may still be debatable, but our results highlight their institutional efforts to increase knowledge about the species in their care.

Tendencias Mundiales en la Producción Investigativa de los Zoológicos y Acuarios Resumen Los zoológicos y los acuarios, con frecuencia considerados empresas de conservación y entretenimiento, también son actores en el esfuerzo por reducir la crisis de la biodiversidad al crear conciencia, apoyar a la conservación y llevar a cabo investigaciones. Evaluamos las tendencias en los temas de investigación y los organismos de estudios en los zoológicos y los acuarios en todo el mundo a través del tiempo. Compilamos los metadatos de las investigaciones realizadas en los zoológicos y acuarios registrados en el Sistema de Manejo de Información Zoológica de Species360 y en la Asociación Mundial de Zoológicos y Acuarios que han sido publicadas en la literatura revisada por pares indexada en Scopus y realizamos un análisis de frecuencias de palabras clave. La producción de artículos científicos por zoológicos se incrementó a una tasa mucho más rápida que la acumulación promedio de artículos científicos en la literatura. La evolución de los temas de investigación fue paralela a la de las ciencias biológicas (p. ej.: desarrollo de la genética molecular o incremento en la conciencia por la conservación). El enfoque del 48.5% de las investigaciones conducidas por los zoológicos estuvo sobre los vertebrados. De este 48.5%, el 33.7% fueron investigaciones sobre mamíferos. Todavía puede debatirse si los zoológicos están contribuyendo efectivamente a la conservación, pero nuestros resultados resaltan sus esfuerzos institucionales por incrementar el conocimiento sobre las especies bajo su cuidado.

Telomere attrition with age in a wild amphibian population.

Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (Epidalea calamita). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout their ontogeny, and that most attrition occurs during the first 1-2 years. We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.

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.

Freshwater macroinvertebrate samples from a water quality monitoring network in the Iberian Peninsula.

This dataset gathers information about the macroinvertatebrate samples and environmental variables collected on rivers of the Ebro River Basin (NE Iberian Peninsula), the second largest catchment in the Iberian Peninsula. The collection is composed of 1,776 sampling events carried out between 2005 and 2015 at more than 400 sampling sites. This dataset is part of a monitoring network set up by the Ebro Hydrographic Confederation, the official body entrusted with the care of the basin, to fulfill the requirements of the European Water Framework Directive. Biological indices based on the freshwater macroinvertebrate communities were used to evaluate the ecological status of the water bodies within the basin. Samples were qualitatively screened for all occurring taxa. Then, all individuals from all taxa in a quantitative subsample of each sample were counted. Biological indices were calculated to estimate water quality at each sampling site. All samples are kept at the Museum of Zoology of the University of Navarra.

The tragedy of the biodiversity data commons: a data impediment creeping nigher?

Researchers are embracing the open access movement to facilitate unrestricted availability of scientific results. One sign of this willingness is the steady increase in data freely shared online, which has prompted a corresponding increase in the number of papers using such data. Publishing datasets is a time-consuming process that is often seen as a courtesy, rather than a necessary step in the research process. Making data accessible allows further research, provides basic information for decision-making and contributes to transparency in science. Nevertheless, the ease of access to heaps of data carries a perception of 'free lunch for all', and the work of data publishers is largely going unnoticed. Acknowledging such a significant effort involving the creation, management and publication of a dataset remains a flimsy, not well established practice in the scientific community. In a meta-analysis of published literature, we have observed various dataset citation practices, but mostly (92%) consisting of merely citing the data repository rather than the data publisher. Failing to recognize the work of data publishers might lead to a decrease in the number of quality datasets shared online, compromising potential research that is dependent on the availability of such data. We make an urgent appeal to raise awareness about this issue.

Reliable effective number of breeders/adult census size ratios in seasonal-breeding species: Opportunity for integrative demographic inferences based on capture-mark-recapture data and multilocus genotypes.

The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales, and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging. The sibship frequency (SF) method is adequate for reliable Nb estimation because it is based on sibship and parentage reconstruction from genetic marker data, thereby providing demographic inferences that can be compared with field-based information. In addition, capture-mark-recapture (CMR) robust design methods are well suited for Na estimation in seasonal-breeding species. We used tadpole genotypes of three pond-breeding amphibian species (Epidalea calamita, Hyla molleri, and Pelophylax perezi, n = 73-96 single-cohort tadpoles/species genotyped at 15-17 microsatellite loci) and candidate parental genotypes (n = 94-300 adults/species) to estimate Nb by the SF method. To assess the reliability of Nb estimates, we compared sibship and parentage inferences with field-based information and checked for the convergence of results in replicated subsampled analyses. Finally, we used CMR data from a 6-year monitoring program to estimate annual Na in the three species and calculate the Nb/Na ratio. Reliable ratios were obtained for E. calamita (Nb/Na = 0.18-0.28) and P. perezi (0.5), but in H. molleri, Na could not be estimated and genetic information proved insufficient for reliable Nb estimation. Integrative demographic studies taking full advantage of SF and CMR methods can provide accurate estimates of the Nb/Na ratio in seasonal-breeding species. Importantly, the SF method provides results that can be readily evaluated for reliability. This represents a good opportunity for obtaining robust demographic inferences with wide applications for evolutionary and conservation research.

Effects of Sample Size and Full Sibs on Genetic Diversity Characterization: A Case Study of Three Syntopic Iberian Pond-Breeding Amphibians.

Accurate characterization of genetic diversity is essential for understanding population demography, predicting future trends and implementing efficient conservation policies. For that purpose, molecular markers are routinely developed for nonmodel species, but key questions regarding sampling design, such as calculation of minimum sample sizes or the effect of relatives in the sample, are often neglected. We used accumulation curves and sibship analyses to explore how these 2 factors affect marker performance in the characterization of genetic diversity. We illustrate this approach with the analysis of an empirical dataset including newly optimized microsatellite sets for 3 Iberian amphibian species: Hyla molleri, Epidalea calamita, and Pelophylax perezi. We studied 17-21 populations per species (total n = 547, 652, and 516 individuals, respectively), including a reference locality in which the effect of sample size was explored using larger samples (77-96 individuals). As expected, FIS and tests for Hardy-Weinberg equilibrium and linkage disequilibrium were affected by the presence of full sibs, and most initially inferred disequilibria were no longer statistically significant when full siblings were removed from the sample. We estimated that to obtain reliable estimates, the minimum sample size (potentially including full sibs) was close to 20 for expected heterozygosity, and between 50 and 80 for allelic richness. Our pilot study based on a reference population provided a rigorous assessment of marker properties and the effects of sample size and presence of full sibs in the sample. These examples illustrate the advantages of this approach to produce robust and reliable results for downstream analyses.

Biodiversity data obsolescence and land uses changes.

BACKGROUND: Primary biodiversity records (PBR) are essential in many areas of scientific research as they document the biodiversity through time and space. However, concerns about PBR quality and fitness-for-use have grown, especially as derived from taxonomical, geographical and sampling effort biases. Nonetheless, the temporal bias stemming from data ageing has received less attention. We examine the effect of changes in land use in the information currentness, and therefore data obsolescence, in biodiversity databases. METHODS: We created maps of land use changes for three periods (1956-1985, 1985-2000 and 2000-2012) at 5-kilometres resolution. For each cell we calculated the percentage of land use change within each period. We then overlaid distribution data about small mammals, and classified each data as 'non-obsolete or 'obsolete,' depending on both the amount of land use changes in the cell, and whether changes occurred at or after the data sampling's date. RESULTS: A total of 14,528 records out of the initial 59,677 turned out to be non-obsolete after taking into account the changes in the land uses in Navarra. These obsolete data existed in 115 of the 156 cells analysed. Furthermore, more than one half of the remaining cells holding non-obsolete records had not been visited at least for the last fifteen years. CONCLUSION: Land use changes challenge the actual information obtainable from biodiversity datasets and therefore its potential uses. With the passage of time, one can expect a steady increase in the availability and use of biological records-but not without them becoming older and likely to be obsolete by land uses changes. Therefore, it becomes necessary to assess records' obsolescence, as it may jeopardize the knowledge and perception of biodiversity patterns.

Mammals in the MZNA Vertebrate Collection of University of Navarra, Spain.

In this paper five datasets are described that provide information about records of mammals in the Vertebrate Collection of the Museum of Zoology of the University of Navarra (MZNA-VERT). The datasets contain 3,466 records belonging to 20 species of mammals sampled across the transition zone between the Atlantic and Mediterranean biogeographical regions (north Iberian Peninsula). The datasets include both distributional data (georeferenced records) and basic biometric data of most of the vouchered specimens stored in the museum facilities. The samples originated mainly within research projects and PhD theses carried out in the former department of Zoology and Ecology of the University of Navarra between 1982 and 2011. The Darwin Core Archive Format datasets are accessible through GBIF.

Long-term data set of small mammals from owl pellets in the Atlantic-Mediterranean transition area.

We describe the pellet sampling data set from the Vertebrate Collection of the Museum of Zoology of the University of Navarra. This data set compiles all information about small mammals obtained from the analysis of owl pellets. The collection consists on skulls, mandibles, and some skeletons of 36 species of more than 72,000 georeferenced specimens. These specimens come from the Iberian Peninsula although most samples were collected in Navarra, a highly diverse transitional area of 10,000 kilometre square sitting across three biogeographical regions. The collection spans more than forty years and is still growing as a result of the establishment of a barn owl pellet monitoring network in 2015. The program will provide critical information about the evolution of the small mammals' community in this transition zone as it changes over time.

Hidalgo Fishes: Dataset on freshwater fishes of Hidalgo state (Mexico) in the MZNA fish collection of the University of Navarra (Spain).

The state of Hidalgo (Mexico) is an important region from the point of view of biodiversity. However, there exists a significant gap in accessible knowledge about species diversity and distribution, especially regarding to freshwater ecosystems. This dataset comprises the sampling records of two projects developed in Hidalgo between 2007 and 2009 about the freshwater fish communities of Tecocomulco lake and rivers belonging to the Metztitlán Canyon Biosphere Reserve. It contains the taxonomic identity (species level) and basic biometric data (total length and weight) as well as date of collection and coordinates of more than 9000 specimens. This dataset is the primary result of the first and unrepeated exhaustive freshwater fish's survey of Metztitlán Canyon Biosphere Reserve and Tecocomulco lake. It incorporates seven more species to the regional fish fauna, and new exclusive biometric data of ten species. This dataset can be used by studies dealing with, among other interests, North American freshwater fish diversity (species richness, distribution patterns) and biometric analyses, useful for the management and conservation of these areas. The complete dataset is also provided in Darwin Core Archive format.