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644 results for “Data Visualizations”
Data from: Host responses to foreign eggs across the avian visual color space
Despite extensive research on the sensory and cognitive processes of host rejection of avian brood parasites' eggs, the underlying perceptual and cognitive mechanisms are not sufficiently understood. Historically, most studies of host egg discrimination assumed that hosts rejected a parasite's egg from their nest based on the total perceived color differences between the parasite's egg and their own. A recent study used a continuous range of parasitic egg colors and discovered that hosts were more likely to reject browner parasitic eggs than parasitic eggs that were more blue-green, even when their absolute perceived color differences from the hosts' own egg colors were similar. However, the extent of these color biases within the avian perceivable color space remains unclear. Therefore, we built upon this previous study by testing European blackbirds' (Turdus merula) responses to model eggs spanning an unprecedented volume of the avian color space. We found that host decisions depended on avian perceived hue, saturation, and luminance of the parasite's egg; hosts generally accepted eggs that were bluer or more blue-green, and more often rejected eggs that were less saturated or darker. We suggest that future studies investigate the underlying mechanism of foreign egg discrimination in other host lineages to determine the prevalence and phylogenetic conservation of such perceptual biases among birds.
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs
Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in both wild and captive populations. NetView P combines data quality control with the construction of population networks based on mutual k-nearest-neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs through multiprocessing in Python. We used the pipeline for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive Silver-lipped Pearl Oysters (n = 415, SNPs = 1107), wild populations of the European Hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and Gray Wolves from North America (n = 239, SNPs = 86,103). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. NetView P comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in Python.
Data from: Visual ecology of true lemurs suggests a cathemeral origin for the primate cone opsin polymorphism
In contrast to the majority of primates, which exhibit dedicated diurnality or nocturnality, all species of Eulemur are cathemeral. Color vision, in particular, is strongly affected by the spectral composition and intensity of ambient light, and the impact of activity period on the evolution of primate color vision is actively debated. We studied three groups of wild brown lemurs (Eulemur fulvus) in Ankarafantsika National Park, Madagascar over a one-year span. We also used non-invasive fecal DNA collection and analysis to study the opsin genes underlying the color vision of 24 individuals. We quantify the color and brightness of dietary fruits and modeled the chromaticity and discriminability of food objects to different visual phenotypes under daylight, twilight, and moonlight conditions. We found that E. fulvus possesses routine dichromacy, unlike its congener E. flavifrons, for which polymorphic trichromacy has been reported. Our models suggest that dichromacy is well-suited to the foraging ecology of E. fulvus. The performance of modeled dichromats and trichromats is comparable under nocturnal illuminants and the luminance values of most diet items are detectable across light conditions. The trichromatic phenotype demonstrates a modest advantage under daylight conditions only. Our results, taken together with reports of polymorphic trichromacy in E. flavifrons, suggest functional ecological variation in the visual system of the genus Eulemur. Interspecific phenotypic variation in the color vision of a genus is both unexpected and instructive. Ecological differences between species of Eulemur could reveal thresholds for the origins of polymorphic trichromacy, which preceded the evolution of routine trichromatic vision in humans and other primates.
Data from: Visual phenotype matching: cues to paternity are present in rhesus macaque faces
The ability to recognize kin and thus behaviourally discriminate between conspecifics based on genetic relatedness is of importance both in acquiring inclusive fitness benefits and to enable optimal inbreeding. In primates, mechanisms allowing recognition of paternal relatives are of particular interest, given that in these mating systems patrilineal information is unlikely to be available via social familiarity. Humans use visual phenotype matching based on facial features to identify their own and other's close relatives, and recent studies suggest similar abilities may be present in other species. However it is unclear to what extent familial resemblances remain detectable against the background levels of relatedness typically found within demes in the wild – a necessary condition if facial cues are to function in kin recognition under natural conditions. Here, we experimentally investigate whether parent-offspring relationships are discernible in rhesus macaque (Macaca mulatta) faces drawn from a large free-ranging population more representative of the latter scenario, and in which genetic relatedness has been well quantified from pedigrees determined via molecular markers. We used the human visual system as a means of integrating multiple types of facial cue simultaneously, and demonstrate that paternal, as well as maternal, resemblance to both sons and daughters can be detected even by human observers. Experts performed better than participants who lacked previous experience working with nonhuman primates. However the finding that even naïve individuals succeeded at the task underlines the strength of the phenotypic cues present in faces.
Data from: Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service
We have reported previously on use of a web-based application, Supramap (http://supramap.org) for the study of biogeographic, genotypic, and phenotypic evolution. Using Supramap we have developed maps of the spread of drug-resistant influenza and host shifts in H1N1 and H5N1 influenza and coronaviruses such as SARS. Here we report on another zoonotic pathogen, H7 influenza, and provide an update on the implementation of Supramap as a web service. We find that the emergence of pathogenic strains of H7 is labile with many transitions from high to low pathogenicity, and from low to high pathogenicity. We use Supramap to put these events in a temporal and geospatial context. We identify several lineages of H7 influenza with biomarkers of high pathogenicity in regions that have not been reported in the scientific literature. The original implementation of Supramap was built with tightly coupled client and server software. Now we have decoupled the components to provide a modular web service for POY (http://poyws.org) that can be consumed by a data provider to create a novel application. To demonstrate the web service, we have produced an application, Geogenes (http://geogenes.org). Unlike in Supramap, in which the user is required to create and upload data files, in Geogenes the user works from a graphical interface to query an underlying dataset. Geogenes demonstrates how the web service can provide underlying processing for any sequence and metadata database.
Data from: MRI-based visualization of rTMS-induced cortical plasticity in the primary motor cortex
<p>Repetitive transcranial magnetic stimulation (rTMS) induces changes in cortical excitability for minutes to hours after the end of intervention. However, it has not been precisely determined to what extent cortical plasticity prevails spatially in the cortex. Recent studies have shown that rTMS induces changes in "interhemispheric" functional connectivity, the resting-state functional connectivity between the stimulated region and the symmetrically corresponding region in the contralateral hemisphere. In the present study, quadripulse stimulation (QPS) was applied to the index finger representation in the left primary motor cortex (M1), while the position of the stimulation coil was constantly monitored by an online navigator. After QPS application, resting-state functional magnetic resonance imaging was performed, and the interhemispheric functional connectivity was compared with that before QPS. A cluster of connectivity changes was observed in the stimulated region in the central sulcus. The cluster was spatially extended approximately 10 mm from the center [half width at half maximum (HWHM): approximately 3 mm] and was extended approximately 20 mm long in depth (HWHM: approximately 7 mm). A localizer scan of the index finger motion confirmed that the cluster of interhemispheric connectivity changes overlapped spatially with the activation related to the index finger motion. These results indicate that cortical plasticity in M1 induced by rTMS was relatively restricted in space and suggest that rTMS can reveal functional dissociation associated with adjacent small areas by inducing neural plasticity in restricted cortical regions.</p>
Data from: Individual variation in cone photoreceptor density in house sparrows: implications for between-individual differences in visual resolution and chromatic contrast
Between-individual variation has been documented in a wide variety of taxa, especially for behavioral characteristics; however, intra-population variation in sensory systems has not received similar attention in wild animals. We measured a key trait of the visual system, the density of retinal cone photoreceptors, in a wild population of house sparrows (Passer domesticus). We tested whether individuals differed from each other in cone densities given within-individual variation across the retina and across eyes. We further tested whether the existing variation could lead to individual differences in two aspects of perception: visual resolution and chromatic contrast. We found consistent between-individual variation in the densities of all five types of avian cones, involved in chromatic and achromatic vision. Using perceptual modeling, we found that this degree of variation translated into significant between-individual differences in visual resolution and the chromatic contrast of a plumage signal that has been associated with mate choice and agonistic interactions. However, there was no evidence for a relationship between individual visual resolution and chromatic contrast. The implication is that some birds may have the sensory potential to perform "better" in certain visual tasks, but not necessarily in both resolution and contrast simultaneously. Overall, our findings (a) highlight the need to consider multiple individuals when characterizing sensory traits of a species, and (b) provide some mechanistic basis for between-individual variation in different behaviors (i.e., animal personalities) and for testing the predictions of several widely accepted hypotheses (e.g., honest signaling).
Data from: High opsin diversity in a non-visual infaunal brittlestar
Background: In metazoans, opsins are photosensitive proteins involved in both vision and non-visual photoreception. Echinoderms have no well-defined eyes but several opsin genes were found in the purple sea urchin (Strongylocentrotus purpuratus) genome. Molecular data are lacking for other echinoderm classes although many species are known to be light sensitive.Results: In this study focused on the European brittle star Amphiura filiformis, we first highlighted a blue-green light sensitivity using a behavioural approach. We then identified 13 new putative opsin genes against eight bona fide opsin genes in the genome of S. purpuratus. Six opsins were included in the rhabdomeric opsin group (r-opsins). In addition, one putative ciliary opsin (c-opsin), showing high similarity with the c-opsin of S. purpuratus (Sp-opsin 1), one Go opsin similar to Sp-opsins 3.1 and 3.2, two basal-branch opsins similar to Sp-opsins 2 and 5, and two neuropsins similar to Sp-opsin 8, were identified. Finally, two sequences from one putative RGR opsin similar to Sp-opsin 7 were also detected. Adult arm transcriptome analysis pinpointed opsin mRNAs corresponding to one r-opsin, one neuropsin and the homologue of Sp-opsin 2. Opsin phylogeny was determined by maximum likelihood and Bayesian analyses. Using antibodies designed against c- and r-opsins from S. purpuratus, we detected putative photoreceptor cells mainly in spines and tube feet of A. filiformis, respectively. The r-opsin expression pattern is similar to the one reported in S. purpuratus with cells labelled at the tip and at the base of the tube feet. In addition, r-opsin positive cells were also identified in the radial nerve of the arm. C-opsins positive cells, expressed in pedicellariae, spines, tube feet and epidermis in S. purpuratus were observed at the level of the spine stroma in the brittle star. Conclusion: Light perception in A. filiformis seems to be mediated by opsins (c- and r-) in, at least, spines, tube feet and in the radial nerve cord. Other non-visual opsin types could participate to the light perception process indicating a complex expression pattern of opsins in this infaunal brittle star.
Data from: Efficacy of visual surveys for white-nose syndrome at bat hibernacula
White-Nose Syndrome (WNS) is an epizootic disease in hibernating bats caused by the fungus Pseudogymnoascus destructans. Surveillance for P. destructans at bat hibernacula consists primarily of visual surveys of bats, collection of potentially infected bats, and submission of these bats for laboratory testing. Cryptic infections (bats that are infected but display no visual signs of fungus) could lead to the mischaracterization of the infection status of a site and the inadvertent spread of P. destructans. We determined the efficacy of visual detection of P. destructans by examining visual signs and molecular detection of P. destructans on 928 bats of six species at 27 sites during surveys conducted from January through March in 2012–2014 in the southeastern USA on the leading edge of the disease invasion. Cryptic infections were widespread with 77% of bats that tested positive by qPCR showing no visible signs of infection. The probability of exhibiting visual signs of infection increased with sampling date and pathogen load, the latter of which was substantially higher in three species (Myotis lucifugus, M. septentrionalis, and Perimyotis subflavus). In addition, M. lucifugus was more likely to show visual signs of infection than other species given the same pathogen load. Nearly all infections were cryptic in three species (Eptesicus fuscus, M. grisescens, and M. sodalis), which had much lower fungal loads. The presence of M. lucifugus or M. septentrionalis at a site increased the probability that P. destructans was visually detected on bats. Our results suggest that cryptic infections of P. destructans are common in all bat species, and visible infections rarely occur in some species. However, due to very high infection prevalence and loads in some species, we estimate that visual surveys examining at least 17 individuals of M. lucifugus and M. septentrionalis, or 29 individuals of P. subflavus are still effective to determine whether a site has bats infected with P. destructans. In addition, because the probability of visually detecting the fungus was higher later in winter, surveys should be done as close to the end of the hibernation period as possible.
Data from: Cryptic differences in colour among Müllerian mimics: how can the visual capacities of predators and prey shape the evolution of wing colours?
Antagonistic interactions between predators and prey often lead to co-evolution. In the case of toxic prey, aposematic colours act as warning signals for predators and play a protective role. Evolutionary convergence in colour patterns among toxic prey evolves due to positive density-dependent selection and the benefits of mutual resemblance in spreading the mortality cost of educating predators over a larger prey assemblage. Comimetic species evolve highly similar colour patterns, but such convergence may interfere with intraspecific signalling and recognition in the prey community, especially for species involved in polymorphic mimicry. Using spectrophotometry measures, we investigated the variation in wing coloration among comimetic butterflies from distantly related lineages. We focused on seven morphs of the polymorphic species Heliconius numata and the seven corresponding comimetic species from the genus Melinaea. Significant differences in the yellow, orange and black patches of the wing were detected between genera. Perceptions of these cryptic differences by bird and butterfly observers were then estimated using models of animal vision based on physiological data. Our results showed that the most strikingly perceived differences were obtained for the contrast of yellow against a black background. The capacity to discriminate between comimetic genera based on this colour contrast was also evaluated to be higher for butterflies than for birds, suggesting that this variation in colour, likely undetectable to birds, might be used by butterflies for distinguishing mating partners without losing the benefits of mimicry. The evolution of wing colour in mimetic butterflies might thus be shaped by the opposite selective pressures exerted by predation and species recognition.
Data from: Olfactory and visual plant cues as drivers of selective herbivory
Food quality is an important consideration in the foraging strategy of all animals, including herbivores. Those that can detect and assess the nutritional value of plants from afar, using senses such as smell and sight, can forage more efficiently than those that must assess food quality by taste alone. Selective foraging not only affects herbivore fitness but can influence the structure and composition of plant communities, yet little is known about how olfactory and visual cues help herbivores to find preferred plants. We tested the ability of a free-ranging, generalist mammalian browser, the swamp wallaby Wallabia bicolor, to use olfactory and visual plant cues to find and/or browse differentially on Eucalyptus pilularis seedlings grown under different nutrient conditions. Low-nutrient seedlings differed from high-nutrient seedlings, having lighter coloured leaves, red stems and lower biomass and nitrogen content. In the absence of visual cues, wallabies used odour to differentiate vials containing cut seedlings. They visited and investigated patches with high-nutrient seedling odour most, followed by patches with low-nutrient seedling odour, and patches with no added odour least. However, when visual and olfactory cues of seedlings were present, wallabies reversed their foraging response and were more likely to browse low- than high-nutrient seedlings. This browsing difference, in turn, disappeared when long-range visual cues were reduced by pinning seedlings horizontal to the ground. We suggest that visual cues overrode the effects of olfactory cues on browsing patterns of intact seedlings. Our study shows that herbivores can respond to odours of higher nutrient plants but in ecologically realistic scenarios they use a variety of visual and olfactory cues, with a context-dependent outcome that is not always selection of high nutrient food. Our results demonstrate the importance of testing the sensory abilities of herbivores in realistic multi-sensory settings to understand their function in selective foraging.
Data from: How lovebirds maneuver through lateral gusts with minimal visual information
Flying birds maneuver effectively through lateral gusts, even when gust speeds are as high as flight speeds. What information birds use to sense gusts and how they compensate is largely unknown. We found that lovebirds can maneuver through 45-degree lateral gusts similarly well in forest, lake, and cave-like visual environments. Despite being diurnal and raised in captivity, the birds fly to their goal perch with only a dim point light source as a beacon, showing that they do not need optic flow or a visual horizon to maneuver. To accomplish this feat, lovebirds primarily yaw their bodies into the gust while fixating their head on the goal using neck angles of up to 30 degrees. Our corroborated model for proportional yaw reorientation and speed control shows how lovebirds can compensate for lateral gusts informed by muscle proprioceptive cues from neck twist. The neck muscles not only stabilize the lovebirds' visual and inertial head orientations by compensating low-frequency body maneuvers, but also attenuate faster 3D wingbeat-induced perturbations. This head stabilization enables the vestibular system to sense the direction of gravity. Apparently, the visual horizon can be replaced by a gravitational horizon to inform the observed horizontal gust compensation maneuvers in the dark. Our scaling analysis shows how this minimal sensorimotor solution scales favorably for bigger birds, offering local wind angle feedback within a wingbeat. The way lovebirds glean wind orientation may thus inform minimal control algorithms that enable aerial robots to maneuver in similar windy and dark environments.
Data from: Dissecting the variation of a visual trait: the proximate basis of UV-Visible reflectance in crab spiders (Thomisidae)
1. The astounding diversity of animal colouration is indicative of a wide variety of selection pressures. Despite great interest in adaptive function, detailed understanding of the constituent elements of colour traits is lacking for many systems. Such information is important in allowing more accurate appraisals of colour variation and its potential production costs. 2. In this study, we 'dissect' the dorsal colour of crab spiders (Thomisidae) to examine the mechanistic basis of a polyphenic colour trait. These spiders possess the ability to alter reflectance in the ultraviolet (UV), violet and blue wavelengths, changing their colour within days. We investigate and compare the proximate mechanistic basis of colour production in multiple phenotypes of three species using histology and spectrophotometry. 3. Our analyses indicate that the spider cuticle is not equivalently transparent to light across the spectrum (300-700 nm) – as previously argued – and contributes to colour variation. UV light is reflected from guanine crystals, present in storage cells ventral to the hypodermis. The crystals are exposed through a partially UV-transmitting hypodermis and cuticle. Variation from white to yellow is likely mediated through pigments/crystals present in different oxidative stages in the hypodermal cells. 4. Simple mechanistic changes are therefore necessary to produce the observed variation, and likely underlie the evolutionary and ontogenetic lability of this trait. Our findings imply that either a UV-reflective abdomen was the ancestral state for crab spiders, or, if pre-dated by UV-absorbent hypodermal pigments, the evolution of UV-reflection has only involved the exposure of underlying guanine crystals through an otherwise clear hypodermis.
Data visualization experiment
Data visualization experiment Source: Objaverse 1.0 / Sketchfab
Color-coded visualization of mpMRI data - Raw observer data
<p>This repository contains raw data from the observer study in the paper: "Color-coded visualization of magnetic resonance imaging multiparametric maps", published in "Scientific Reports", 2016. For details on the data, please refer to the paper or contact JN Kather (http://orcid.org/0000-0002-3730-5348).</p>
Color-coded visualization of mpMRI data - visualization results
<p>This repository contains raw data from the paper: "Color-coded visualization of magnetic resonance imaging multiparametric maps", published in "Scientific Reports", 2016. For details on the data, please refer to the paper or contact JN Kather directly (http://orcid.org/0000-0002-3730-5348).</p> <p>All image files are provided as DICOM files (fully anonymized). Please note that not all DICOM viewers are capable of displaying RGB images. If the images in the "Trivariate" channel are not shown in color, please try the OsiriX free DICOM viewer (http://www.osirix-viewer.com).</p>
Data to: "Distinct Neural Components of Visually Guided Grasping during Planning and Execution"
<p>This record contains experimental and analysis scripts (written in Matlab) as well as raw and processed data to reproduce the results shown in:</p><p>Klein LK<strong>†</strong>, Maiello G<strong>†</strong>, Stubbs KM, Proklova D, Chen J, Paulun VC, Culham JC, Fleming RW (2023) Distinct neural components of visually guided grasping during planning and execution. <i>Journal of Neuroscience.</i> <a href="https://doi.org/10.1523/JNEUROSCI.0335-23.2023">10.1523/JNEUROSCI.0335-23.2023</a>.<i> <strong>†</strong>Co-first author</i></p>
Scripts for data analysis and visualization of GOTM-FABM-BFM simulations at the BOUSSOLE site
<p>Model output, data and scripts to reproduce results in Álvarez et al. (2023): Chromophoric dissolved organic matter dynamics revealed through the optimization of a spectrally and vertically resolved model in the NW Mediterranean Sea.</p>
Analysis of two focus groups about data visualization
<p>This repository contains two datasets concerning the analysis of two focus groups about data visualization.</p> <ul> <li><strong>frequency_matrix_v2.xlsx: </strong>this resource contains a frequency analysis matrix of the focus groups. The categories are identified on the horizontal axis, using different colours according to the hierarchy of the categorical system (meta-category, categories, and subcategories) to facilitate the subsequent axial coding of the content.</li> <li><strong>content_matrix_v2.xlsx: </strong>this resource contains the analysis of the content of the two focus groups. Following data reduction, the ideas or units of analysis about each category were grouped and coded. In this way, the content analysis was completed with the coding of the units of analysis about the respective categories using the axial coding procedure.</li> <li><strong>Transcription_experts_ES.pdf: </strong>this document is the original transcription of the focus group discussion with experts in Spanish.</li> <li><strong>Transcription_experts_EN.pdf: </strong>this document is a transcription of the focus group discussion with experts, automatically translated into English by DeepL.</li> <li><strong>Transcription_phd_ES.pdf: </strong>this document is the original transcription of the focus group discussion with Ph.D. students in Spanish.</li> <li><strong>Transcription_phd_EN.pdf: </strong>this document is a transcription of the focus group discussion with Ph.D. students, automatically translated into English by DeepL.</li> </ul>
Data for "Visualizing thickness-dependent magnetic textures in few-layer Cr2Ge2Te6"
<p>Data from all the figures in the main text of "Visualizing thickness-dependent magnetic textures in few-layer Cr2Ge2Te6". All files contain the data displayed in the paper and are in *.fig format (MATLAB). They can be opened using MATLAB.</p>
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.