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1,163 results for “demonstration”
Data from: Noninvasive physiological markers demonstrate link between habitat quality, adult sex ratio and poor population growth rate in a vulnerable species, the Cape mountain zebra
Effective conservation and species management requires an understanding of the causes of poor population growth. Conservation physiology uses biomarkers to identify factors that contribute to low individual fitness and population declines. Building on this, macrophysiology can use the same markers to assess how individual physiology varies with different ecological or demographic factors over large temporal and spatial scales. Here, we use a macrophysiological approach to identify the ecological and demographic correlates of poor population growth rates in the Cape mountain zebra metapopulation. We use two non-invasive biomarkers: faecal glucocorticoids as a measure of chronic stress, and faecal androgens as an indicator of male physiological status. We found that faecal glucocorticoid concentrations were highest in the spring prior to summer rainfall, and were elevated in individuals from populations associated with low quality habitat (lower grass abundance). In addition, faecal androgen concentrations were higher in populations with a high proportion of non-breeding stallions (where male:female adult sex ratios exceed 2:1) suggesting sex ratio imbalances may intensify male competition. Finally, population growth rate was negatively associated with faecal glucocorticoid concentrations and female fecundity was negatively associated with faecal androgens, indicating a relationship between hormone profiles and fitness. Together, our results provide cross population evidence for how poor population growth rates in Cape mountain zebra can be linked to individual physiological biomarkers. More broadly, we advocate physiological biomarkers as indicators of population viability, and as a way to evaluate the impact of variable ecological and demographic factors. In addition, conservation physiology can be used to assess the efficacy of management interventions for this subspecies, and this approach could inform models of species' responses to future environmental change.
Data from: An experimental demonstration that house finches add cigarette butts in response to ectoparasites
Urban species encounter resources that are uncommon in nature, such as materials found in city waste. Many studies have shown that these can be harmful to wildlife. In Mexico City, house finches bring cigarette butts to their nests, which reduces the amount of ectoparasites, but also induces genotoxic damage in chicks and parents. Yet, the reason for this behaviour is unknown. One possibility is that birds extract the cellulose fibres from discarded butts simply because they resemble feathers. Alternatively, disassembled cigarette butts may be brought to the nests because they repel ectoparasites. Here we tested the latter hypothesis by assessing whether house finches Carpodacus mexicanus increase the amount of cigarette butts in their nests in response to a raise in ectoparasite load. When present, fibres from butts are concentrated in the nest lining. By taking it away, we simultaneously removed most of the butt material and collected the bulk of the tick population infesting each nest, as these parasites cluster in the lining. We removed the bedding of nests when chicks had recently hatched, and randomly assigned each nests to one of the following treatments: 1) addition of live ticks, 2) addition of dead ticks and 3) simulation of tick addition. Females in the live ticks' treatment added more butt fibres to their nests than parents in control treatments. Additionally, the amount of butt fibres in the original lining also predicted the amount of fibres added after the manipulation. It seems that the tendency to bring to the nest cigarette butts is at least partially a response to current, and perhaps also past, parasite load.
Data from: A single session of hyperbaric oxygen therapy demonstrates acute and long-lasting neuroplasticity effects in humans: a replicated, randomized controlled clinical trial
Purpose: Animal studies have demonstrated anti-inflammatory, and anti-nociceptive properties of hyperbaric oxygen therapy (HBOT). However, physiological data are scarce in humans. In a recent experimental study, the authors used the burn injury (BI) model observing a decrease in secondary hyperalgesia area (SHA) in the HBOT-group compared to a control-group.Surprisingly, a long-lasting neuroplasticity effect mitigating the BI-induced SHA-response was seen in the HBOT-preconditioned group. The objective of the present study, therefore, was to confirm our previous findings using an examiner-blinded, block-randomized, controlled, crossover study design. Patients and methods: Nineteen healthy subjects attended two BI-sessions with an inter-session interval of ≥28 days. The BIs were induced on the lower legs by a contact thermode (12.5 cm2, 47C°, 420 s). The subjects were block-randomized to receive HBOT (2.4 ATA, 100% O2, 90 min) or ambient conditions ([AC]; 1 ATA, 21% O2), dividing cohorts equally into two sequence allocations: HBOT-AC or AC-HBOT. All sensory assessments performed during baseline, BI, and post-intervention phases were at homologous time points irrespective of sequence allocation. The primary outcome was SHA, comparing interventions and sequence allocations. Data are mean (95% CI). Results: During HBOT-sessions a mitigating effect on SHAs was demonstrated compared to AC-sessions, ie, 18.8 (10.5–27.0) cm2 vs 32.0 (20.1–43.9) cm2 (P=0.021), respectively. In subjects allocated to the sequence AC-HBOT a significantly larger mean difference in SHA in the AC-session vs the HBOT-session was seen 25.0 (5.4–44.7) cm2 (P=0.019). In subjects allocated to the reverse sequence, HBOT-AC, no difference in SHA between sessions was observed (P=0.55), confirming a preconditioning, long-lasting (≥28 days) effect of HBOT. Conclusion: Our data demonstrate that a single HBOT-session compared to control is associated with both acute and long-lasting mitigating effects on BI-induced SHA, confirming central anti-inflammatory, neuroplasticity effects of hyperbaric oxygen therapy.
Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)
The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K–Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1–3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K–Pg mass extinction, in the Paleocene–Eocene (65.5–33.9 Ma) or in association with the Eocene–Oligocene transition (33.9 Ma).
Data from: Demonstration of pollinator-mediated competition between two native Impatiens species, Impatiens noli-tangere and I. textori (Balsaminaceae)
Plant–plant interspecific competition via pollinators occurs when the flowering seasons of two or more plant species overlap and the pollinator fauna is shared. Negative sexual interactions between species (reproductive interference) through improper heterospecific pollen transfer have recently been reported between native and invasive species demonstrating pollination-driven competition. We focused on two native Impatiens species (I. noli-tangere and I. textori) found in Japan and examined whether pollinator-mediated plant competition occurs between them. We demonstrate that I. noli-tangere and I. textori share the same pollination niche (i.e., flowering season, pollinator fauna, and position of pollen on the pollinator's body). In addition, heterospecific pollen grains were deposited on most stigmas of both I. noli-tangere and I. textori flowers that were situated within 2 m of flowers of the other species resulting in depressed fruit set. Further, by hand-pollination experiments, we show that when as few as 10% of the pollen grains are heterospecific, fruit set is decreased to less than half in both species. These results show that intensive pollinator-mediated competition occurs between I. noli-tangere and I. textori. This study suggests that intensive pollinator-mediated competition occurs in the wild even when interacting species are both native and not invasive.
Data from: Seeds in motion: genetic assignment and hydrodynamic models demonstrate concordant patterns of seagrass dispersal
Movement is fundamental to the ecology and evolutionary dynamics within species. Understanding movement through seed dispersal in the marine environment can be difficult due to the high spatial and temporal variability of ocean currents. We employed a mutually enriching approach of population genetic assignment procedures and dispersal predictions from a hydrodynamic model to overcome this difficulty and quantify the movement of dispersing floating fruit of the temperate seagrass Posidonia australis Hook.f. across coastal waters in southwestern Australia. Dispersing fruit cohorts were collected from the water surface over two consecutive years and seeds were genotyped using microsatellite DNA markers. Likelihood-based genetic assignment tests were used to infer the meadow of origin for seed cohorts and individuals. A three-dimensional hydrodynamic model was coupled with a particle transport model to simulate the movement of fruit at the water surface. Floating fruit cohorts were mainly assigned genetically to the nearest meadow, but significant genetic differentiation between cohort and most-likely meadow of origin suggested a mixed origin. This was confirmed by genetic assignment of individual seeds from the same cohort to multiple meadows. The hydrodynamic model predicted 60% of fruit dispersed within 20 km, but that fruit were physically capable of dispersing beyond the study region. Concordance between these two independent measures of dispersal provide insight into the role of physical transport for long distance dispersal (LDD) of fruit and the consequences for spatial genetic structuring of seagrass meadows.
Data from: Empirical demonstration of hybrid chromosomal races in house mice
Western house mice (Mus musculus domesticus) and common shrews (Sorex araneus) are important models for study of chromosomal speciation. Both had ancestral karyotypes consisting of telocentric chromosomes, and each is subdivided into numerous chromosomal races many of which have resulted from fixation of new mutations (Robertsonian fusions and whole-arm reciprocal translocations). However, some chromosomal races in both species may alternatively have originated through hybridization, with particular homozygous recombinant products reaching fixation. Here, we demonstrate the process of generation of hybrid chromosomal races for the first time in either species using molecular markers. Analysis of centromeric microsatellite markers show that the Mid Valtellina (IMVA) and Upper Valtellina (IUVA) chromosomal races of the house mouse are recombinant products of hybridization of the Lower Valtellina (ILVA) and Poschiavo (CHPO) chromosomal races, supporting earlier theoretical analysis. IMVA and IUVA occupy a small area of the Italian Alps where ILVA makes contact with CHPO. IUVA and CHPO have previously been shown to be reproductively isolated in one village, emphasizing that hybrid chromosomal races in small mammals, as in plants, have the potential to be part of the speciation process.
Data from: Oviposition site choice under conflicting risks demonstrates that aquatic predators drive terrestrial egg-laying
Laying eggs out of water was crucial to the transition to land and has evolved repeatedly in multiple animal phyla. However, testing hypotheses about this transition has been difficult because extant species only breed in one environment. The pantless treefrog, Dendropsophus ebraccatus, makes such tests possible because they lay both aquatic and arboreal eggs. Here, we test the oviposition site choices of D. ebraccatus under conflicting risks of arboreal egg desiccation and aquatic egg predation, thereby estimating the relative importance of each selective agent on reproduction. We also measured discrimination between habitats with and without predators and development of naturally laid aquatic and arboreal eggs. Aquatic embryos in nature developed faster than arboreal embryos, implying no cost to aquatic egg laying. In choice tests, D. ebraccatus avoided habitats with fish, showing that they can detect aquatic egg predators. Most importantly, D. ebraccatus laid most eggs in the water when faced with only desiccation risk, but switched to laying eggs arboreally when desiccation risk and aquatic predators were both present. This provides the first experimental evidence to our knowledge that aquatic predation risk influences non-aquatic oviposition and strongly supports the hypothesis that it was a driver of the evolution of terrestrial reproduction.
Data from: Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics.
The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multi-locus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multi-locus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as OTUs, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.
Data from: Male courtship preferences demonstrate discrimination against allopatric colour morphs in a cichlid fish
Whether premating isolation is achieved by male-specific, female-specific or sex-independent assortative preferences often depends on the underlying evolutionary processes. Here we test mate preferences of males presented with females of different allopatric colour variants of the cichlid fish Tropheus, a Lake Tanganyika endemic with rich geographic colour pattern variation, in which the strength of sexual isolation varies between populations. We conducted two-way mate choice experiments to compare behaviour of males of a red-bodied morph (population Moliro) towards females from their own population with behaviour towards females from four allopatric populations at different stages of phylogenetic and phenotypic divergence. Males courted same-population females significantly more intensely than females of other populations, and reduced their heteromorphic courtship efforts both with increasing genetic and increasing phenotypic distinctness of the females. In particular, females of a closely related red-bodied population received significantly more courtship than either genetically distinct, similarly coloured females ("Kirschfleck" morph) or genetically related, differently coloured females ("yellow-blotch" morph), both of which were courted similarly. Genetically and phenotypically distinct females (T. polli) were not courted at all. Consistent with previous female-choice experiments, female courtship activity also decreased with increasing genetic distance from the males' population. Given successful experimental and natural introgression between colour morphs and the pervasive allopatry of related variants, we consider it unlikely that assortative preferences of both sexes were driven by direct selection during periods of secondary contact or, in turn, drove colour pattern differentiation in allopatry. Rather, we suggest that sexual isolation evolved as by-product of allopatric divergence.
Videos for demonstration
<p>These are videos in which the results are overlaid on the original from-camera videos. Please turn to the section 3.2 and the legend of Fig. 7b for the explanation of the inset(s) of "MovieS1" and "MovieS2".</p>
Amber fossils demonstrate deep-time stability of Caribbean lizard communities
<p>This is the dataset for the paper Sherratt et al. 2015 (PNAS, doi: ). Included are the X-ray microtomography (micro-CT) TIFF stacks for the amber encased anole lizard fossils studied. Also included are the morphometric data for the fossil and 100 modern specimens, and the phylogenetic character matrix for the fossils and 181 species (91 morphological characters, 4873 DNA bases).</p> <p>Abstract</p> <p>Whether the structure of ecological communities can exhibit stability over macroevolutionary timescales has long been debated. The similarity of independently evolved <em>Anolis</em> lizard communities on environmentally similar Greater Antillean islands supports the notion that community evolution is deterministic. However, a dearth of Caribbean <em>Anolis</em> fossils—only three have been described to date—has precluded direct investigation of the stability of anole communities through time. Here we report on an additional 17 fossil anoles in Dominican amber dating to 15–20 My before the present. Using data collected primarily by X-ray micro computed tomography (X-ray micro-CT), we demonstrate that the main elements of Hispaniolan anole ecomorphological diversity were in place in the Miocene. Phylogenetic analysis yields results consistent with the hypothesis that the ecomorphs that evolved in the Miocene are members of the same ecomorph clades extant today. The primary axes of ecomorphological diversity in the Hispaniolan anole fauna appear to have changed little between the Miocene and the present, providing evidence for the stability of ecological communities over macroevolutionary timescales.</p>
Demonstration of AutoPost surface tracking plugin - NAB 2016
<p>The AutoPost Consortium presents in this video a demostration of a close-to-final version of the surface tracking plugin developed within the project on a challenging VFX task (adding a tattoo to the upper arm).</p> <p>You can also enjoy the video at AutoPost <a href="https://vimeo.com/165140518">Vimeo channel</a></p> <p>AutoPost project is co-funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 644629.</p>
AutoPost matting plugin demonstration - NAB 2016
<p>The AutoPost Consortium presents a demonstration of a prototype of the alpha matting plugin developed within the project on a challenging VFX task (replacing the background of a scene with a complex background).</p> <p>You can enjoy the video at <a href="http://vimeo.com/autopost"> AutoPost Vimeo channel </a> </p> <p>AutoPost project is co-funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 644629.</p>
The weather workflow used in demonstration of the VFramework
<p>The weather workflow used in demonstration of the VFramework.</p> <p>The package contains context model for two executions.</p> <p>The workflow is also included.</p>
ECOSSIAN Irish Demonstration Video
<p>This video aims at illustrating the Irish use case related to the gas network sector.</p>
Dataset for NXmpes demonstration
<p>Dataset for the generation of Nexus files using the Nomad Nexus parser</p>
Demonstration of Portable Performance of Scientific Machine Learning on High Performance Computing Systems
<p>With the largest datasets to date and a diverse set of discoveries to be made, the current generation of scientific analyses are well poised to utilize artificial intelligence (AI) and machine learning (ML) on high performance computing (HPC) resources. Like never before, these workflows can be written in one portable language, python, which thanks to highly-optimized ML libraries achieves excellent cross-platform performance with little to no intervention by the user. In this demonstration, we explore the performance of several scientific AI/ML applications across leading HPC resources and highlight best practices for portable performance.</p>
Fig. 4 in NC-Clustering demonstrates heterospecificity of the cryptic ant species Temnothorax luteus (FOREL, 1874) and T. racovitzai (BONDROIT, 1918) (Hymenoptera: Formicidae)
Fig. 4: Temnothorax luteus (FOREL, 1874) in lateral view; shown is the type of the junior synonym Temnothorax
Fig. 3 in NC-Clustering demonstrates heterospecificity of the cryptic ant species Temnothorax luteus (FOREL, 1874) and T. racovitzai (BONDROIT, 1918) (Hymenoptera: Formicidae)
Fig. 3: Head of Temnothorax luteus (FOREL, Fig. 5: Head of lectotype of Temnothorax racovitzai (BONDROIT, 1918).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.