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8,537 results for “Openness”
Data from: The bright incubate at night: sexual dichromatism and adaptive incubation division in an open-nesting shorebird
Ornamentation of parents poses a high risk for offspring because it reduces cryptic nest defence. Over a century ago, Wallace proposed that sexual dichromatism enhances crypsis of open-nesting females although subsequent studies found that dichromatism per se is not necessarily adaptive. We tested whether reduced female ornamentation in a sexually dichromatic species reduces the risk of clutch depredation and leads to adaptive parental roles in the red-capped plover Charadrius ruficapillus, a species with biparental incubation. Males had significantly brighter and redder head coloration than females. During daytime, when visually foraging predators are active, colour-matched model males incurred a higher risk of clutch depredation than females, whereas at night there was no difference in depredation risk between sexes. In turn, red-capped plovers maintained a strongly diurnal/nocturnal division of parental care during incubation, with males attending the nest largely at night when visual predators were inactive and females incubating during the day. We found support for Wallace's conclusion that reduced female ornamentation provides a selective advantage when reproductive success is threatened by visually foraging predators. We conclude that predators may alter their prey's parental care patterns and therefore may affect parental cooperation during care.
Data from: Habitat preference facilitates successful early breeding in an open-cup nesting songbird
Selecting breeding habitats that ameliorate environmental limits on fitness and facilitate successful reproduction should benefit individual animals. This is particularly true in the temperate zone, where breeding early in a season presents a unique series of environmental challenges that can limit an individual's fitness. While many studies document links between habitat quality and reproductive success, few identify the cues used to assess habitat quality or the components of reproduction most influenced by occupying higher quality habitat, particularly during the early breeding season. We used detailed spatial maps and observations of all early season nesting attempts in an insular song sparrow (Melospiza melodia) population over 38 years to estimate the influence of nest-site preference on reproductive success and to test whether relative microclimate or food availability may act as cues for early season site selection. Female sparrows in preferred early season nest sites had earlier laying dates, exhibited more energetically efficient incubation behaviour and produced more offspring that recruited to the population than those nesting in less-preferred sites. Preference for potential nesting sites was positively related to leaf damage by Lepidopteran larvae, an indicator of food abundance, negatively related to early season microclimate, likely due to greater vegetation cover, and unrelated to site-specific plant phenology. Our findings show that breeding in preferred, high-quality habitat may offer females a fitness advantage by facilitating early laying and the production of offspring more likely to recruit to the population at a lower potential reproductive cost to the parent. We provide a clear demonstration of potential links between habitat preference and quality and their contributions to the ecology and life history of animals in seasonal environments.
Data from: Fire-induced population reduction and landscape opening increases gene flow via pollen dispersal in Pinus halepensis
Population reduction and disturbances may alter dispersal, mating patterns and gene flow. Rather than taking the common approach of comparing different populations or sites, here we studied gene flow via wind-mediated effective pollen dispersal on the same plant individuals before and after a fire-induced population drop, in a natural stand of Pinus halepensis. The fire killed 96% of the pine trees in the stand and cleared the vegetation in the area. Thirteen trees survived in two groups separated by ~80 m, and seven of these trees had serotinous (closed) pre-fire cones that did not open despite the fire. We analyzed pollen from closed pre- and post-fire cones using microsatellites. The two groups of surviving trees were highly genetically differentiated, and the pollen they produced also showed strong among-group differentiation and very high kinship both before and after the fire, indicating limited and very local pollen dispersal. The pollen not produced by the survivors also showed significant pre-fire spatial genetic structure and high kinship, indicating mainly within-population origin and limited gene flow from outside, but became spatially homogeneous with random kinship after the fire. We suggest that post-fire gene flow via wind-mediated pollen dispersal increased by two putative mechanisms: 1) a drastic reduction in local pollen production due to population thinning, effectively increasing pollen immigration; 2) an increase in wind speeds in the vegetation-free post-fire landscape. This research shows that dispersal can alleviate negative genetic effects of population size reduction, and that disturbances might enhance gene flow, rather than reduce it.
Data from: Open water camouflage via 'leaky' light guides in the midwater squid Galiteuthis
Galiteuthis, a midwater squid, has photophores on the ventral surfaces of its eyes. These photophores emit bioluminescence to counter-illuminate the shadows cast by the eyes in downwelling sunlight, thereby hiding the eyes from upward-looking predators. The photophores consist of laminated fibre-like cells with semi-coaxial protein-dense layers around axial cytoplasm. These cells have been suggested to function as light guides: bioluminescence is an isotropic process used to hide in an anisotropic light environment, so any emission must be reshaped to be effective. We found a wide variation in cross-sectional geometries of photophore cells; some were more efficient at light guiding than others. We used a set of optical models to place these photophores in the context of the radiance where Galiteuthis lives and discovered a possible adaptive reason for this variation. In Galiteuthis's horizontal and vertical range, ocean radiance is also quite variable. For complete camouflage, photophores must reproduce this variation in radiance using an isotropic source. Our models show that variation in the geometry of the photophore light guides reproduces the predicted variation in ocean radiance experienced by this species. By selectively activating geometrically distinct populations of photophore cells, the animal may reproduce the angular distribution of light at all positions in its habitat.
Data from: AudioMoth: evaluation of a smart open acoustic device for monitoring biodiversity and the environment
1. The cost, usability and power efficiency of available wildlife monitoring equipment currently inhibits full ground-level coverage of many natural systems. Developments over the last decade in technology, open science, and the sharing economy promise to bring global access to more versatile and more affordable monitoring tools, to improve coverage for conservation researchers and managers. 2. Here we describe the development and proof-of-concept of a low-cost, small-sized and low-energy acoustic detector: 'AudioMoth'. The device is open-source and programmable, with diverse applications for recording animal calls or human activity at sample rates of up to 384kHz. We briefly outline two ongoing real-world case studies of large-scale, long-term monitoring for biodiversity and exploitation of natural resources. These studies demonstrate the potential for AudioMoth to enable a substantial shift away from passive continuous recording by individual devices, towards smart detection by networks of devices flooding large and inaccessible ecosystems. 3. The case studies demonstrate one of the smart capabilities of AudioMoth, to trigger event logging on the basis of classification algorithms that identify specific acoustic events. An algorithm to trigger recordings of the New Forest cicada (Cicadetta montana) demonstrates the potential for AudioMoth to vastly improve the spatial and temporal coverage of surveys for the presence of cryptic animals. An algorithm for logging gunshot events has potential to identify a shotgun blast in tropical rainforest at distances of up to 500 m, extending to 1km with continuous recording. 4. AudioMoth is more energy efficient than currently available passive acoustic monitoring (PAM) devices, giving it considerably greater portability and longevity in the field with smaller batteries. At a build cost of ~US$43 per unit, AudioMoth has potential for varied applications in large-scale, long-term acoustic surveys. With continuing developments in smart, energy-efficient algorithms and diminishing component costs, we are approaching the milestone of local communities being able to afford to remotely monitor their own natural resources.
Data from: Evolution of Dendrocolaptes platyrostris (Aves: Furnariidae) between the South American open vegetation corridor and the Atlantic forest
The open vegetation corridor of South America is a region dominated by savanna biomes. It contains forests, i.e. riverine forests, that may act as corridors for rainforest specialist between the open vegetation corridor and its neighboring biomes, the Amazonian and Atlantic forests. A prediction for this scenario is that populations of rainforest specialists in the open vegetation corridor and in the forested biomes show no significant genetic divergence. We addressed this hypothesis by studying plumage and genetic variation of the Planalto woodcreeper Dendrocolaptes platyrostris Spix (1824) (Aves: Furnariidae), a forest specialist that occurs in both the open habitat and in the Atlantic forest. Our questions are: (1) is there any evidence of genetic continuity between populations of the open habitat and the Atlantic forest? and (2) is plumage variation congruent with patterns of neutral genetic structure or with ecological factors related to habitat type? We used cytochrome b and mtDNA control region sequences to show that D. platyrostris is monophyletic and that presents substantial intraspecific differentiation. We found two areas of plumage stability: one associated to Cerrado and the other associated to southern Atlantic Forest. Multiple Mantel tests showed that most of the plumage variation followed transition of habitats but not phylogeographic gaps, suggesting that selection may be related to the evolution of the species plumage. Results were not compatible with the idea that forest specialist in the open vegetation corridor and in the Atlantic forest are linked at the population level because birds from each region were not part of the same genetic unit. Divergence in the presence of gene flow across the ecotone between both regions might explain our results. Also, our findings indicate that the southern Atlantic forest may have been significantly affected by Pleistocene climatic alteration, but that those events did not cause local extinction of most taxa, as occurred in other regions of the globe where forests were significantly affected by global glaciations. Finally, our results neither supported subspecies nor regions of stability of plumage as species.
Data from: Single-dose oral ciprofloxacin prophylaxis as a response to a meningococcal meningitis epidemic in the African meningitis belt: a three-arm, open-label, cluster-randomized trial
Background: Antibiotic prophylaxis for contacts of meningitis cases is not recommended during outbreaks in the African meningitis belt. We assessed the effectiveness of single-dose oral ciprofloxacin administered to household contacts and in village-wide distributions on the overall attack rate (AR) in an outbreak of meningococcal meningitis. Methods and findings: In this 3-arm, open-label, cluster-randomized trial during a meningococcal meningitis outbreak in Madarounfa District, Niger, villages notifying a suspected case were randomly assigned (1:1:1) to standard care (the control arm), single-dose oral ciprofloxacin for household contacts within 24 hours of case notification, or village-wide distribution of ciprofloxacin within 72 hours of first case notification. The primary outcome was the overall AR of suspected meningitis after inclusion. A random sample of 20 participating villages was enrolled to document any changes in fecal carriage prevalence of ciprofloxacin-resistant and extended-spectrum beta-lactamase (ESBL)–producing Enterobacteriaceae before and after the intervention. Between April 22 and May 18, 2017, 49 villages were included: 17 to the control arm, 17 to household prophylaxis, and 15 to village-wide prophylaxis. A total of 248 cases were notified in the study after the index cases. The AR was 451 per 100,000 persons in the control arm, 386 per 100,000 persons in the household prophylaxis arm (t test versus control p = 0.68), and 190 per 100,000 persons in the village-wide prophylaxis arm (t test versus control p = 0.032). The adjusted AR ratio between the household prophylaxis arm and the control arm was 0.94 (95% CI 0.52–1.73, p = 0.85), and the adjusted AR ratio between the village-wide prophylaxis arm and the control arm was 0.40 (95% CI 0.19‒0.87, p = 0.022). No adverse events were notified. Baseline carriage prevalence of ciprofloxacin-resistant Enterobacteriaceae was 95% and of ESBL-producing Enterobacteriaceae was >90%, and did not change post-intervention. One limitation of the study was the small number of cerebrospinal fluid samples sent for confirmatory testing. Conclusions: Village-wide distribution of single-dose oral ciprofloxacin within 72 hours of case notification reduced overall meningitis AR. Distributions of ciprofloxacin could be an effective tool in future meningitis outbreak responses, but further studies investigating length of protection, effectiveness in urban settings, and potential impact on antimicrobial resistance patterns should be carried out.
Data from: Accuracy of genomic selection models in a large population of open-pollinated families in white spruce
Genomic selection (GS) is of interest in breeding because of its potential for predicting the genetic value of individuals and increasing genetic gains per unit of time. To date, very few studies have reported empirical results of GS potential in the context of large population sizes and long breeding cycles such as for boreal trees. In this study, we assessed the effectiveness of marker-aided selection in an undomesticated white spruce (Picea glauca (Moench) Voss) population of large effective size using a GS approach. A discovery population of 1694 trees representative of 214 open-pollinated families from 43 natural populations was phenotyped for 12 wood and growth traits and genotyped for 6385 single-nucleotide polymorphisms (SNPs) mined in 2660 gene sequences. GS models were built to predict estimated breeding values using all the available SNPs or SNP subsets of the largest absolute effects, and they were validated using various cross-validation schemes. The accuracy of genomic estimated breeding values (GEBVs) varied from 0.327 to 0.435 when the training and the validation data sets shared half-sibs that were on average 90% of the accuracies achieved through traditionally estimated breeding values. The trend was also the same for validation across sites. As expected, the accuracy of GEBVs obtained after cross-validation with individuals of unknown relatedness was lower with about half of the accuracy achieved when half-sibs were present. We showed that with the marker densities used in the current study, predictions with low to moderate accuracy could be obtained within a large undomesticated population of related individuals, potentially resulting in larger gains per unit of time with GS than with the traditional approach.
Data from: Soft-surface grasping: radular opening in Aplysia californica
Grasping soft, irregular material is challenging both for animals and robots. The feeding systems of many animals have adapted to this challenge. In particular, the feeding system of the marine mollusk, Aplysia californica, a generalist herbivore, allows it to grasp and ingest seaweeds of varying shapes, textures and toughness. On the surface of Aplysia's grasper is a structure known as the radula, a thin flexible cartilaginous sheet with fine teeth. Previous in vitro studies suggested that an intrinsic muscle, I7, is responsible for opening the radula. Lesioning I7 in vivo does reduce opening width, but does not prevent animals from grasping and ingesting food. New in vitro studies demonstrate that a set of fine muscle fibers on the ventral surface of the radula, the subradular fibers (SRFs), mediate opening movements even if the I7 muscles are absent. Both in vitro and in vivo lesions demonstrate that removing the subradular fibers leads to profound deficits in radular opening, and significantly reduces feeding efficiency. A theoretical biomechanical analysis of the actions of the subradular fibers suggests that they induce the radular surface to open around a central crease in the radular surface and to arch the radular surface, allowing it to softly conform to irregular material. A three-dimensional model of the radular surface, based on in vivo observations and magnetic resonance imaging of intact animals, provides support for the biomechanical analysis. These results suggest how a soft grasper can work during feeding, and suggest novel designs for artificial soft graspers.
Data from: Ophthalmologic evaluation of severely obese patients undergoing bariatric surgery: a pilot, monocentric, prospective, open-label study
Purpose: The aim of this study was to investigate the pathogenic role of obesity on blinding eye diseases in a population of severely obese patients with no history of eye diseases, and to verify whether weight loss induced by bariatric surgery may have a protective effect. Methods: This was a pilot, monocentric, prospective, and open label study conducted at the University Hospital of Pisa. Fifty-seven severely obese patients with a mean body mass index value of 44.1 ± 6 kg/m2 were consecutively recruited and received a complete ophthalmological evaluation and optical coherence tomography. Twenty-nine patients who underwent gastric bypass were evaluated also 3 months, and 1 year after surgery. Results: At baseline, blood pressure value were directly and significantly related to intraocular pressure values (p<0.05, R = 0.35). Blood pressure values were also significantly and inversely related to retinal nerve fiber layer thickness, particularly in the temporal sector (RE p<0.05 r-0.30; LE p<0.01, R = -0.43). Moreover, minimum foveal thickness values were significantly and inversely associated with body mass index (RE p<0.02, R = -0.40; LE p<0.02, R = -0.30). A significant reduction of body mass index (p<0.05) and a significant (p<0.05) improvement of blood pressure was observed three months and one year after gastric bypass, which were significantly associated with an increase in retinal nerve fiber layer thickness and minimum foveal thickness values in both eyes (p<0.05). Conclusions: The results of this study suggest that obese patients may have a greater susceptibility to develop glaucomatous optic nerve head damage and age-related macular degeneration. Moreover, weight reduction and improvement of comorbidities obtained by bariatric surgery may be effective in preventing eye disease development by improving retinal nerve fiber layer and foveal thickness.
Data from: Candelariella clarkii and Lecidea hoganii: two lichen species new to science from White Rocks Open Space, City of Boulder, Colorado
Two new species are described from vouchers collected as part of an intensive lichen inventory of Fox Hills Sandstone outcrops in an open space preserve within the city limits of Boulder, Colorado. Candelariella clarkii is characterized by its cryptolecanorine apothecia, chartreuse areolate thallus, and 8-spored asci. Lecidea hoganii is a member of the L. auriculata morphological group characterized by a thick white chalky thallus, pink pigments in the hymenium, and absence of secondary compounds. We provide IUCN conservation assessments for both new species, which should be considered critically endangered. The discovery of two species new to science in a relatively densely populated region of North America illustrates the ecological relevance of small of patches of native habitat, which are certain to become even more important in the future.
Data from: An R package for analyzing survival using continuous-time open capture-recapture models
Capture–recapture software packages have proven to be very powerful tools for analysing factors affecting survival in wild populations. However, all such packages are limited to discrete-time protocols. Appropriate survival analysis tools are still lacking for data acquired from continuous-time protocols. We have developed a statistical method and propose an r package for analysing such data based on an extension of classical survival analysis models incorporating an inhomogeneous Poisson process for modelling capture histories. First, data were simulated from a continuous-time protocol. These data were used to (i) compare survival estimation biases of discrete- and continuous-time approaches and (ii) investigate the performance and accuracy of our r package for four types of covariates: factors varying between individuals (like sex), in time (like climatic factors), both in time and between individuals (like physical condition) and age (as a categorical factor). Secondly, the r package has been applied to a real data set for survival analysis of cats in the Kerguelen archipelago (regrouping 682 cats over 20 years) as an illustrative example. Results of the simulated data analysis show that the method performs better than its discrete-time counterpart for analysing data acquired from continuous-time protocols. It provides unbiased parameter estimates for all parameters except those that vary both in time and between individuals – which is not surprising, since in our case, these factors were not updated in continuous time (i.e. only upon capture). When applied to the Kerguelen cat data set, the results suggest that survival is lower in juveniles than in adults and subadults, varies between study sites and increases with physical condition, and this latter effect being more important in females than in males. Sex, season, temporal linear trend in survival and the NDVI vegetation index were also tested but were not found to be significant. However, confidence intervals were too large (due to a low recapture rate) for excluding such effects. Further analyses are still needed for rigorous covariate testing in this context. In conclusion, continuous-time approaches – such as that presented in this paper – should be preferred when data acquired from continuous-time protocols is analysed.
Data from: Evolutionary radiations of Proteaceae are triggered by the interaction between traits and climates in open habitats
Aim: Ecologically driven diversification can create spectacular diversity in both species numbers and form. However, the prediction that the match between intrinsic (e.g. functional trait) and extrinsic (e.g. climatic niche) variables may lead to evolutionary radiation has not been critically tested. Here, we test this hypothesis in the Southern Hemisphere plant family Proteaceae, which shows a spectacular diversity in open mediterranean shrublands in the Southwest Australian Floristic Region (SWAFR) and the Cape Floristic Region (CFR). Species in the Proteaceae family occupy habitats ranging from tropical rain forests to deserts and are remarkably variable in leaf morphology. Location: Southern Hemisphere. Methods: We built a phylogenetic tree for 337 Proteaceae species (21% of the total), representing all main clades, climatic tolerances and morphologies, and collected leaf functional traits (leaf area, sclerophylly, leaf shape) for 261 species and climatic niche data for 1645 species. Phylogenetic generalized least squares regression and quantitative-trait evolutionary model testing were used to investigate the evolutionary pathways of traits and climatic niches, and their effect on diversification rates. Results: We found that divergent selection may have caused lineages in open vegetation types to evolve towards trait and climatic niche optima distinct from those in closed forests. Furthermore, we show that the interaction between open habitats, dry, warm and/or mediterranean climates, and small, sclerophyllous, toothed leaves increases net diversification rates in Proteaceae. Main conclusions: Our results suggest that the evolution of specific leaf adaptations may have allowed Proteaceae to adapt to variable climatic niches and diversify extensively in open ecosystems such as those in the CFR and SWAFR. This match between morphology and environment may therefore more generally lead to evolutionary radiation.
Data from: OpenNahele: the open Hawaiian forest plot database
This data paper provides a description of OpenNahele, the open Hawaiian forest plot database. OpenNahele includes 530 forest plots across the Hawaiian archipelago containing 43,590 individuals of 185 native and alien tree, shrub and tree fern species across six islands. We include estimates of maximum plant size (D950.1 and Dmax3) for 58 woody plant species, a key functional trait associated with dispersal distance and competition for light. OpenNahele can serve as a platform to test key ecological, evolutionary and conservation questions in a hotspot archipelago.
Grand Opening Scissors
Grand opening scissors i made for a grand opening scene Source: Objaverse 1.0 / Sketchfab
2013 Open Data Barometer
<p>The Open Data Barometer aims to uncover the true prevalence and impact of open data initiatives around the world. It analyses global trends, and also ranks countries and regions via an in-depth methodology that considers: readiness to secure the benefits of open data; actual levels of implementation; and the impact of such initiatives.</p> <p>This is the pilot edition of the Open Data Barometer, and contains data from a global expert survey, along with secondary data.</p> <p>Full details are provided in the Open Data Barometer 2013 Global Report</p>
Open Access to Excellent Science - the European Research Council's approach (video recording)
<p>Video recording of a presentation given at the event 'Open Access: Authors, publishers, investors and institutions for the dissemination of the scientific research's results' that was organised by the Library of EPFL in the context of the Open Access Week 2013. The video includes the introduction of the presentation by EPFL Director, Dr. Isabelle Kratz.</p> <p><strong>Abstract</strong>: We will give an overview of the ERC's approach to Open Access, and how it is reflected in the rules governing the ERC grants under the current 7th EU Research Framework Programme. We will explain how the ERC supports its grantees in providing open access to their research results, and shed some light on the changes to be expected for the new EU Research Framework Programme, Horizon 2020, which will start on 1 January 2014. In doing so, we will also take a look at the different roles of the ERC and the European Commission concerning the promotion of Open Access, and explain some of the differences in approach.</p>
SCAD-zbMATH-01 Open Access Data Set for Author Name Disambiguation (AND) (Enhanced Version)
<p>This data set contains disambiguated publication data from zbMATH (www.zbmath.org) for use in author name disambiguation (AND). It covers 28321 publications with 33810 authorship records, authored by 2946 distinct authors. Authorship records have been manually annotated with author identifiers.</p> <p>This download includes additional data sets for advanced, selective disambiguation.</p> <p>For details, see "Mark-Christoph Müller, Florian Reitz, and Nicolas Roy (2017): Data Sets for Author Name Disambiguation: An Empirical Analysis and a New Resource", Scientometrics, doi:10.1007/s11192-017-2363-5.</p> <p> </p>
Online Appendix for "An Exploratory Study of the State of Practice of Performance Testing in Java-Based Open Source Projects"
<p>Here we collect some raw data and additional material to the paper <em>"An Exploratory Study of the State of Practice of Performance Testing in Java-Based Open Source Projects"</em>, by Philipp Leitner and Cor-Paul Bezemer.</p>
FIGURE 2 in A new species of Ischnocnema (Anura: Eleutherodactylinae) from open areas of the Cerrado Biome in southeastern Brazil
FIGURE 2. Ischnocnema penaxavantinho sp. n.. above left: holotype (male, ZUEC 13639), Above right: a topotype (male, AAG-UFU 4124), below: a specimen from Perdizes–MG tentatively attributed to the new species (male, AAG- UFU 2616).
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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.