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Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Spain

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_ES_20200204: >> Agencia Espaola de Consumo, Seguridad Alimentaria y Nutricin >> Ministerio de Agricultura, Pesca y Alimentacin

Specific monitoring results of ESBL-/AmpC-/carbapenemase-producing bacteria and specific monitoring of carbapenemase-producing bacteria, in the absence of isolates detected complementing the European Union Overview Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2017/2018

This dataset derives from the specific monitoring of E. coli producers of ESBLs/AmpC/carbapenemases, as well as the specific monitoring of carbapenemase-producers (voluntary reporting), in the absence of any isolates detected. This dataset contains only data when Total units positive equals zero '0'.

Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Cyprus

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_CY_20200204: >> Ministry of Agriculture, Natural Resources and Evironment - Veterinary Services

Antimicrobial resistance monitoring results complementing the EU Overview Summary Report on AMR in zoonotic and indicator bacteria from humans, animals and food in 2017/2018 - Iceland

This dataset contains AMR monitoring results in animals and food at the isolate level pursuant to Article 9 of Directive 2003/99/EC and to Annex, part B, of Commission implementing Decision 2013/652/EU. In addition, the dataset includes any other results from isolates than the ones mentioned in the Commission implementing Decision 2013/652/EU. The quantitative minimum inhibitory concentration (MIC) data from dilution methods are included. REPORTING AUTHORITIES CONTRIBUTING TO EACH DATA COLLECTION: AMR_2018_IS_20200204: >> Icelandic Food and Veterinary Authority

opencc-zeroJul 2020View details →

Data from: A meta-analysis of factors influencing the strength of mate choice copying in animals

Davies et al., (2020) All data and R code Mate-choice copying is a form of social learning in which an individual's choice of mate is influenced by the apparent choices of other individuals of the same sex, and has been observed in more than 20 species across a broad taxonomic range. Though fitness benefits of copying have proven difficult to measure, theory suggests that copying should not be beneficial for all species or contexts. However, the factors influencing the evolution and expression of copying have proven difficult to resolve. We systematically searched the literature for studies of mate-choice copying in non-human animals, and then performed a phylogenetically-controlled meta-analysis to explore which factors influence the expression of copying across species. Across 58 published studies in 23 species, we find strong evidence that animals copy the mate choice of others. The strength of copying was significantly influenced by taxonomic group, however sample size limitations mean it is difficult to draw firm conclusions regarding copying in mammals and arthropods. The strength of copying was also influenced by experimental design: copying was stronger when choosers were tested before and after witnessing a conspecific's mate choice, compared to when choosers with social information were compared to choosers without. Importantly, we did not detect any difference in the strength of copying between males and females, or in relation to the rate of multiple mating. Our search also highlights that more empirical work is needed to investigate copying in a broader range of species, especially those with differing mating systems and levels of reproductive investment.

opencc-zeroAug 2020View details →

How biological invasions affect animal behaviour: a global, cross-taxonomic analysis

1. In the Anthropocene, species are faced with drastic challenges due to rapid, human-induced changes, such as habitat destruction, pollution and biological invasions. In the case of invasions, native species may change their behaviour to minimise the impacts they sustain from invasive species, and invaders may also adapt to the conditions in their new environment in order to survive and establish self-sustaining populations. 2. We aimed at giving an overview of which changes in behaviour are studied in invasions, and what is known about the types of behaviour that change, the underlying mechanisms and the speed of behavioural changes. 3. Based on a review of the literature, we identified 191 studies and 360 records (some studies reported multiple records) documenting behavioural changes caused by biological invasions in native (236 records from 148 species) or invasive (124 records from 50 species) animal species. This global dataset, which we make openly available, is not restricted to particular taxonomic groups. 4. We found a mild taxonomic bias in the literature towards mammals, birds and insects. In line with the enemy release hypothesis, native species changed their anti-predator behaviour more frequently than invasive species. Rates of behavioural change were evenly distributed across taxa, but not across types of behaviour. 5. Our findings may help to better understand the role of behaviour in biological invasions as well as temporal changes in both population densities and traits of invasive species, and of native species affected by them.

opencc-by-4.0Aug 2020View details →

3-D animation of water current in the pharynx of an Appendicularian

Seawater enters the mouth and flows ventrally to a pair of spiracles (gill apertures) that open ventrally. Food particles (in red) are retained by the pharyngeal filter and water (in blue) exits though the spiracles to the outside of the body.

opencc-zeroSep 2020View details →

How to build a dinosaur: musculoskeletal modelling and simulation of locomotor biomechanics in extinct animals

The intersection of paleontology and biomechanics can be reciprocally illuminating, helping to improve paleobiological knowledge of extinct species and furthering our understanding of the generality of biomechanical principles derived from study of extant species. However, working with data gleaned primarily from the fossil record has its challenges. Building on decades of prior research, we outline and critically discuss a complete workflow for biomechanical analysis of extinct species, using locomotor biomechanics in the Triassic theropod dinosaur Coelophysis as a case study. We progress from the digital capture of fossil bone morphology to creating rigged skeletal models, to reconstructing musculature and soft tissue volumes, to the development of computational musculoskeletal models, and finally to the execution of biomechanical simulations. Using a three-dimensional musculoskeletal model comprising 33 muscles, a static inverse simulation of the mid-stance of running shows that Coelophysis probably used more upright (extended) hindlimb postures, and was likely capable of withstanding a vertical ground reaction force of magnitude more than 2.5 times body weight. We identify muscle force-generating capacity as a key source of uncertainty in the simulations, highlighting the need for more refined methods of estimating intrinsic muscle parameters such as fibre length. Our approach emphasizes the explicit application of quantitative techniques and physics-based principles, which helps maximize results robustness and reproducibility. Although we focus on one specific taxon and question, many of the techniques and philosophies explored here have much generality to them, so they can be applied in biomechanical investigation of other extinct organisms.

opencc-zeroOct 2019View details →

Data from: No consistent effects of humans on animal genetic diversity worldwide

Human impacts on genetic diversity are poorly understood yet critical to biodiversity conservation. We used 175,247 COI sequences collected between 1980 and 2016 to assess the global effects of land use and human density on the intraspecific genetic diversity of 17,082 species of birds, fishes, insects, and mammals. Human impacts on mtDNA diversity were taxon and scale-dependent, and were generally weak or non-significant. Spatial analyses identified weak latitudinal diversity gradients as well as negative effects of human density on insect diversity, and negative effects of intensive land use on fish diversity. The observed effects were predominantly associated with species turnover. Time series analyses found nearly an equal number of positive and negative temporal trends in diversity, resulting in no net monotonic trend in diversity over this time period. Our analyses reveal critical data and theory gaps and call for increased efforts to monitor global genetic diversity.

opencc-by-4.0Oct 2020View details →

VFTS meeting: animation of main-sequence model evolution

This animation shows the evolution of our binary and single stellar models from 2Myr to 100Myr. We populate 3763 binaries, whose primary mass is in the range of 3Msun to 100Msun, following a Salpeter IMF with an exponent of -2.37. The mass ratio is uniformly distributed from 0.1 to 1. The orbital period logP is uniformly distributed from the minimum value at which the two stars would contact initially to 3.5. Both components rotate at half of their critical velocities initially.  Considering a binary fraction of 70%, we populate 1612 single stars with vi=0.5. In addition, we also populate 537 slowly-rotating single stars with vi=0.2 to reproduce the observed blue MS in young star clusters. The number is chosen such that the ratio between the slow and fast rotators is 1/3, which is the same as the ratio of observed blue and red MS stars.  Gravity darkening and observational errors are included. Filled circles correspond to single stellar models, while open symbols correspond to binaries with different companions. Single stellar tracks with vi=0.5 are plotted with solid grey lines. The black dotted line represents the ZAMS line of vi=0.2 single stellar models. In the legend, the number in each group outside the parenthesis corresponds to the number of stars whose color and magnitude are in the figure range. While the number in the parenthesis corresponds to the number of stars above the orange dashed line, which is 1.75 mag below the turn-off magnitude.

opencc-zeroOct 2020View details →

Plant-animal interactions between carnivorous plants, sheet-web spiders, and ground-running spiders as guild predators in a wet meadow community

Plant-animal interactions are diverse and wide-spread shaping ecology, evolution and biodiversity of most ecological communities. Carnivorous plants are unusual in that they can be simultaneously engaged with animals in multiple mutualistic and antagonistic interactions including reversed plant-animal interactions where they are the predator. Competition with animals is a potential antagonistic plant-animal interaction unique to carnivorous plants when they and animal predators consume the same prey. The goal of this field study was to test the hypothesis that under natural conditions, sundews and spiders are predators consuming the same prey thus creating an environment where interkingdom competition can occur. Over 12 months, we collected data on 15 dates in the only protected Highland Rim Wet Meadow Ecosystem in Kentucky where sundews, sheet-web spiders and ground-running spiders co-exist. One each sampling day, we attempted to locate fifteen sites with: 1) both sheet-web spiders and sundews; 2) sundews only; and where neither occurred. Sticky traps were set at each of these sites to determine prey (springtails) activity-density. Ground-running spiders were collected on sampling days. DNA extraction was performed on all spiders to determine which individuals had eaten springtails and comparing this to the density of sundews where the spiders were captured. Sundews and spiders consumed springtails. Springtail activity-densities were lower the higher the density of sundews. Both sheet-web and ground-running spiders were found less often where sundew densities were high. Sheet-web size was smaller where sundews densities were high. The results of this study suggest that asymmetrical exploitative competition occurs between sundews and spiders. Sundews appear to have a greater negative impact on spiders, where spiders probably have little impact on sundews. In this example of interkingdom competition where the asymmetry should be most extreme, amensalism where one competitor experiences no cost of interaction may be occurring.

opencc-by-4.0Oct 2020View details →

Animation of finite-time coherent sets in the Agulhas region

This animation shows finite-time coherent sets that were detected in the Agulhas region with the OPTICS clustering method applied to simulated Lagrangian particles. Clusters are determined based on the first 100 days of trajectory data. The corresponding trajectory data can be found here: https://doi.org/10.5281/zenodo.3899942.

opencc-zeroOct 2020View details →

Weight loss, insulin resistance, and study design confound results in a meta-analysis of animal models of fatty liver

The classical drug development pipeline necessitates studies using animal models of human disease to gauge future efficacy in humans, however there is a low conversion rate from success in animals to humans. Non-alcoholic fatty liver disease (NAFLD) is a complex chronic disease without any established therapies and a major field of animal research. We performed a meta-analysis with meta-regression of 603 interventional rodent studies (10,364 animals) in NAFLD to assess which variables influenced treatment response. Weight loss and alleviation of insulin resistance were consistently associated with improvement in NAFLD. Multiple drug classes that do not affect weight in humans caused weight loss in animals. Other study design variables, such as age of animals and dietary composition, influenced the magnitude of treatment effect. Publication bias may have increased effect estimates by 37-79%. These findings help to explain the challenge of reproducibility and translation within the field of metabolism.

opencc-zeroNov 2020View details →

Data from: Morphological characters can strongly influence early animal relationships inferred from phylogenomic data sets

There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: The sister to all other Metazoa (SOM). Here we use published phylogenomic datasets (∼45,000-400,000 characters in size with ∼15-100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological datasets (∼15-275 characters). We additionally use small exemplar datasets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, i.e. likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, i.e., that genomic-scale datasets will swamp out inferences from morphological data. Instead, weighting morphological data 2-10× in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular datasets (>200,000 characters and up to ∼100 taxa) showing node stability even with ≧100× up-weighting of morphological data. Accordingly, our analyses have three strong messages. A) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined datasets, even when outnumbered thousands of times by morphological data. Morphology therefore should not be counted out a priori. B.) We here quantify for the first time how the stability of the SOM node improves for several genomic datasets when the taxon sampling is increased. C.) The patterns of "flipping points" (i.e., the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of datasets that should be developed into a new sensitivity analysis tool.

opencc-by-4.0Nov 2020View details →

Animated GIF of simulated plume and virtual flight tracks

The animated GIF shows the dispersion of an exhaust plume modelled with WRF 3.8.1 as a large eddy simulation, as well as virtual cross sectional flight tracks, in the left panel. The right panel shows the emission rates retrieved by the virtual cross sectional overflights. Every two minutes a virtual measurement is performed. The daily solar irradiation causes a deep, convective boundary layer with turbulent plume dispersion within. In the nocturnal absence of solar irradiation, the boundary layer shrinks, leading to narrow, homogeneous plume dispersion, within a laminar flow.

opencc-zeroDec 2020View details →

Conspicuous animal signals avoid the cost of predation by being intermittent or novel: confirmation in the wild using hundreds of robotic prey

Social animals are expected to face a trade-off between producing a signal that is detectible by mates and rivals, but not obvious to predators. This trade-off is fundamental for understanding the design of many animal sig- nals, and is often the lens through which the evolution of alternative communication strategies is viewed. We have a reasonable working knowl- edge of how conspecifics detect signals under different conditions, but how predators exploit conspicuous communication of prey is complex and hard to predict. We quantified predation on 1566 robotic lizard prey that per- formed a conspicuous visual display, possessed a conspicuous ornament or remained cryptic. Attacks by free-ranging predators were consistent across two contrasting ecosystems and showed robotic prey that performed a conspicuous display were equally likely to be attacked as those that remained cryptic. Furthermore, predators avoided attacking robotic prey with a fixed, highly visible ornament that was novel at both locations. These data show that it is prey familiarity—not conspicuousness—that determine predation risk. These findings replicated across different preda- tor–prey communities not only reveal how conspicuous signals might evolve in high predation environments, but could help resolve the paradox of aposematism and why some exotic species avoid predation when invad- ing new areas.

opencc-by-4.0Dec 2020View details →

Animations: The Photospheric Footpoints of Solar Coronal Hole Jets

This repository provides the individual animations of the SDO/AIA and HMI magnetograms of Jets 1, 2, 3, corresponding to jets 14, 32, 35 in Table 1 of the accepted manuscript, "The Photospheric Footpoints of Solar Coronal Hole Jets".  jet1-aia193.mp4:   AIA 193A movie of Jet 1 jet1-hmimag.mp4:   HMI magnetograms movie of Jet 1 jet1-aia193-hmi-contour.mp4:   AIA 193A with HMI contours movie of Jet 1 fig1anim.mp4:   Concatenation of Jet 1 movies shown in Figure 1 of the accepted manuscript. jet2-aia193.mp4:   AIA 193A movie of Jet 2 jet2-hmimag.mp4:   HMI magnetograms movie of Jet 2 jet2-aia193-hmi-contour.mp4:   AIA 193A with HMI contours movie of Jet 2 fig4anim.mp4:   Concatenation of Jet 2 movies shown in Figure 4 of the accepted manuscript. jet3-aia193.mp4:   AIA 193A movie of Jet 3 jet3-aia304.mp4:   AIA 304A movie of Jet 3 jet3-hmimag.mp4:   HMI magnetograms movie of Jet 3 jet3-aia193-hmi-contour.mp4:   AIA 193A with HMI contours movie of Jet 3 fig6anim.mp4:   Concatenation of Jet 3 movies shown in Figure 6 of the accepted manuscript.

opencc-by-4.0Dec 2020View details →

Supplementary materials for article focused on traffic information enrichment: Animation and complete overview of all road segments on which basis summary test results were calculated

Supplementary materials (Appendix A and B) for the article: Traffic Information Enrichment: Creating Long-Term Traffic Speed Prediction Ensemble Model for Better Navigation through Waypoints Abstract: Traffic speed prediction for a selected road segment from a short-term and long-term perspective is among the fundamental issues of intelligent transportation systems (ITS). During the course of the past two decades, many artefacts (e.g., models) have been designed dealing with traffic speed prediction. However, no satisfactory solution has been found for the issue of a long-term prediction for days and weeks using the vast spatial and temporal data. This article aims to introduce a long-term traffic speed prediction ensemble model using country-scale historic traffic data from 37,002 km of roads, which constitutes 66% of all roads in the Czech Republic. The designed model comprises three submodels and combines parametric and nonparametric approaches in order to acquire a good-quality prediction that can enrich available real-time traffic information. Furthermore, the model is set into a conceptual design which expects its usage for the improvement of navigation through waypoints (e.g., delivery service, goods distribution, police patrol) and the estimated arrival time. The model validation is carried out using the same network of roads, and the model predicts traffic speed in the period of 1 week. According to the performed validation of average speed prediction at a given hour, it can be stated that the designed model achieves good results, with mean absolute error of 4.67 km/h. The achieved results indicate that the designed solution can effectively predict the long-term speed information using large-scale spatial and temporal data, and that this solution is suitable for use in ITS. Simunek, M., & Smutny, Z. (2021). Traffic Information Enrichment: Creating Long-Term Traffic Speed Prediction Ensemble Model for Better Navigation through Waypoints. Applied Sciences, 11(1), 315. <a href="https://doi.org/10.3390/app11010315">https://doi.org/10.3390/app11010315</a>   Appendix A Examples of the deviation between the average speed and the FreeFlowSpeed for selected hours.   Appendix B The text file provides a complete overview of all road segments on which basis summary test results were calculated in Section 6 of the article.

opencc-zeroDec 2020View details →

Data from: Pushing Raman spectroscopy over the edge: purported signatures of organic molecules in fossil animals are instrumental artefacts

Widespread preservation of fossilized biomolecules in many fossil animals has recently been reported in six studies, based on Raman microspectroscopy. Here, we show that the putative Raman signatures of organic compounds in these fossils are actually instrumental artefacts resulting from intense background luminescence. Raman spectroscopy is based on the detection of photons scattered inelastically by matter upon its interaction with a laser beam. For many natural materials, this interaction also generates a luminescence signal that is often orders of magnitude more intense than the light produced by Raman scattering. Such luminescence, coupled with the transmission properties of the spectrometer, induced quasi-periodic ripples in the measured spectra that have been incorrectly interpreted as Raman signatures of organic molecules. Although several analytical strategies have been developed to overcome this common issue, Raman microspectroscopy as used in the studies questioned here cannot be used to identify fossil biomolecules.