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4,356 results for “RED”
Schrödinger's Red Pixel by Quasi Bound-States-In-the-Continuum
<p>The uploaded dataset contains the raw data and codes for the paper to be published on Science Advances, with the manuscript title of "Schrödinger’s Red Pixel by Quasi Bound-States-In-the-Continuum".</p>
Unmapped reds: Another lesson from unmapped reads – in depth analysis of RNA-Seq reads from various horse tissues
<p>Unmapped reds – all RNA-Seq reads that did not map to the reference EquCab3.0 genome using Tophat2 software</p> <p>Data: loin adipose - AD, hoof lamina - LM, liver - LI, longissimus muscle - LO, left lung - LU, heart left ventricle - LV, ovary- OV and parietal cortex – PC<br> 1 – horse ECA_UCD_AH1<br> 2 – horse ECA_UCD_AH2</p>
Monthly and seasonal climatologies of the mixed layer potential temperature and salinity budgets in the Red Sea
<p>Monthly and seasonal climatologies of the mixed layer temperature and salinity budgets in the Red Sea (RS), analyzed using the outputs of a high-resolution (1/100) ocean general circulation model (MITgcm) covering the period 2001 to 2015 (Krokos et al., 2021).</p> <p>The data support the analysis presented in the paper "Processes governing the seasonal evolution of mixed layers in the Red Sea", accepted for publication in the Journal of Geophysical Research - Oceans.</p> <p>The model diagnostics’ terms include the mixed layer depth (MLD), the surface heat (Qnet) and freshwater fluxes (FW), the mixed layer pot. temperature (MLT) and salinity (MLS), and the surface velocities over the RS.</p> <p>The analyzed budget terms include the tendency of pot. temperature θ and salinity S (TT, ST), the surface fluxes of θ and S (TF, SF), the divergence of the advective fluxes of θ and S (TA, SA), the diffusive flux of θ and S (TD, SD), and processes at the ML base (Tbase, Sbase) that comprise en(de)trainment and the advective and diffusive fluxes acting on the en(de)trained volume.</p> <p>Krokos, G., Cerovečki, I., Zhan, P., Hendershott, M. C., & Hoteit, I. (2021). Seasonal Evolution of Mixed Layers in the Red Sea and the Relative Contribution of Atmospheric Buoyancy and Momentum Forcing, 1–44. Retrieved from http://arxiv.org/abs/2112.08762</p>
White Blood Cells with cytoplasm and surrounding red blood cells
<p>This dataset is taken from doi:10.17632/w7cvnmn4c5.1 and is used for segmentation of irregular shaped white blood cells in 2D. We also provide dataset for cytoplasm and we trained StarDist and UNET models to be applied in the VollSeg setting on this dataset.</p>
Declining survival rates of red foxes (Vulpes vulpes) during the first outbreak of sarcoptic mange in Sweden
<p>Rapid declines in red fox (Vulpes vulpes) populations have followed outbreaks of epizootic mange caused by the mite Sarcoptes scabiei. In Sweden, the first outbreak of sarcoptic mange started in 1977/78 and affected the whole country by 1984. Here we used data on number of harvested red foxes from Gävleborg county (18 199 km2) in Sweden between 1970 and 1994. We used data on the prevalence of sarcoptic mange in harvested red foxes from 1974 to 1982. A rapid decline in harvested foxes occurred two to three years after the prevalence of sarcoptic mange first became evident. In the same period, Mark-Recovery data were used to estimate changes in survival rates, and the best model included an effect of age (young or adult) and period (annual) on the survival and recapture probabilities. The analysis was based data from 701 young foxes of which 523 were recovered, and 133 adults of which 131 were recovered. Average annual survival was 0.55 (range=0.53-0.58) for adult and 0.36 (range=0.32-0.39) for young foxes in the three years preceding the outbreak. During the outbreak and the remaining six years of the study, the average survival was reduced to 0.41 (range=0.30-0.48) for adult and to 0.25 (range=0.17-0.30) for young foxes. A population model, based on our results on survival and literature data on fecundity, was developed to project the decline of the fox population. The rate and magnitude of the reduction in the projected population and harvested foxes were similar, with both reduced by almost ninety percent. Harvest statistics indicate the fox population recovered to pre-mange densities in less than 10 years after the first detection of mange indicating a rapid development of resistance in the host. This study shows the importance of long-term population monitoring in combination with large-scale field-experiments to device alternative management options.</p>
Complex genetic patterns and distribution limits mediated by native congeners of the worldwide invasive red‐eared slider turtle
<p>Non-native (invasive) species offer a unique opportunity to study the geographic distribution and range limits of species, wherein the evolutionary change driven by interspecific interactions between native and non-native closely related species is a key component. The red-eared slider turtle, <i>Trachemys scripta elegans</i> (TSE), has been introduced and successfully established worldwide. It can coexist with its native congeners <i>T. cataspila</i>, <i>T. venusta</i> and <i>T. taylori</i> in Mexico. We performed comprehensive fieldwork, executed a battery of genetic analyses and applied a novel species distribution modeling approach to evaluate their historical lineage relationships and contemporary population genetic patterns. Our findings support the historical common ancestry between native TSE and non-native (TSE<sub>alien</sub>), while also <span>highlighting the genetic differentiation of the exotic lineage. G</span>enetic patterns are associated with their range size/endemism gradient, the microendemic <i>T. taylori</i> showed significant reduced genetic diversity and high differentiation, whereas TSE<sub>alien</sub><span> showed </span>the highest diversity and signals of population size expansion. Counter to our expectations, <span>lower naturally occurring distribution overlap and little admixture patterns </span>were found<span> between TSE and its congeners, exhibiting reduced gene flow and clear genetic separation across neighboring species despite having zones of contact. We demonstrate that</span> these native <i>Trachemys</i> species have distinct climatic niche suitability, likely preventing establishment of and displacement by the TSE<sub>alien</sub>. Moreover, we <span>found </span>major niche overlap between TSE<sub>alien </sub>and native species worldwide, supporting our prediction that sites with closer ecological optima to the invasive species have higher establishment risk than those that are closer to the niche-center of the native species.</p>
Global flyway evolution in red knots Calidris canutus and genetic evidence for a Nearctic refugium
<p>Present-day ecology and population structure are the legacies of past climate and habitat perturbations, and this is particularly true for species that are widely distributed at high latitudes. The red knot, <em>Calidris canutus</em>, is an arctic-breeding, long-distance migratory shorebird with six recognized subspecies defined by differences in morphology, migration behavior, and annual-cycle phenology, in a global distribution thought to have arisen just since the Last Glacial Maximum (LGM). We used nextRAD sequencing of 10,881 single-nucleotide polymorphisms (SNPs) to assess the neutral genetic structure and phylogeographic history of 172 red knots representing all known global breeding populations. Using population genetics approaches, including model-based scenario-testing in an approximate Bayesian computation (ABC) framework, we infer that red knots derive from two main lineages that diverged ca. 34,000 years ago, and thus most likely persisted at the LGM in both Palearctic and Nearctic refugia, followed by at least two instances of secondary contact and admixture. Within two Beringian subspecies (<em>C. c. roselaari</em> and <em>rogersi</em>), we detected previously unknown genetic structure among sub-populations sharing a migratory flyway, reflecting additional complexity in the phylogeographic history of the region. Conversely, we found very weak genetic differentiation between two Nearctic populations (<em>rufa</em> and <em>islandica</em>) with clearly divergent migratory phenotypes and little or no apparent contact throughout the annual cycle. Together, these results suggest that relative gene flow among migratory populations reflects a complex interplay of historical, geographical, and ecological factors.</p>
Genetic structure in the nonbreeding range of rufa Red Knots suggests distinct Arctic breeding populations
<p>An understanding of the migratory connectivity between breeding and nonbreeding areas is fundamental to the management of long-distance migrants under pressure from habitat change along their flyways. Here we describe evidence for genetic structure within the nonbreeding range of the endangered Arctic-Canadian rufa subspecies of Red Knots (Calidris canutus). Using blood and tissue samples from the major nonbreeding regions in Argentina (Tierra del Fuego and Río Negro), northern Brazil (Maranhão), and southeastern USA (Florida), we estimated genetic structure in 514 amplified fragment length polymorphism (AFLP) loci, applying cluster assignment analyses in DAPC, assignPOP, and STRUCTURE. Using a priori location information, individuals could be correctly re-assigned to their nonbreeding regions, which validated that the assignment accuracy of the data was sufficient. Without using a priori location information, we detected 3–5 genotype clusters, and posterior assignment probabilities of samples to these genotype clusters varied among the three regions. Lastly a chi-square test confirmed that allele frequencies varied significantly among nonbreeding regions, rejecting the hypothesis that samples were drawn from a single gene pool. Our findings hint at undescribed structure within the Red Knot rufa breeding range in the Canadian Arctic and indicate that each rufa nonbreeding area in this study hosts a different subsample of these breeding populations. The observation that nonbreeding sites of rufa Red Knots contain different genetic pools argues for separate conservation management of these sites.</p>
Importance of hematite self-reversal in Al-rich soils magnetostratigraphy: Revisiting the Damei red soil sequence in the Bose Basin, southern China
<p>This is the data of the article titled "<strong>Importance of hematite self-reversal in Al-rich soils magnetostratigraphy: Revisiting the Damei red soil sequence in the Bose Basin, southern China</strong>" which submitted for publication to JGR-Solid Earth under the reference # 2021JB023165</p>
African Red Slip Ware Digital (ARS3D) - Comparison-Data
<p>Characteristic of the North African bowls, plates, and jugs are their pictorial decorations applied mainly by appliqués and stamps. As mass-produced image carriers and everyday objects, the ARS spread throughout the empire.</p> <p>The range of motifs includes mythological scenes as well as scenes from the Old and New Testament, circus, arena and hunting scenes as well as fish and plant motifs. The appliqués-decorated pottery thus provides insights into Late Antique imagination and its changes, as well as into the economic history of the period between the 3rd and 5th centuries AD in North Africa.</p> <p>Previous documentation methods were not able to capture the objects and their decoration in an adequate way. The digital recording of the RGZM's collections by 3D scans allows to compare potentially identical appliqués and to assign them to their negative forms and the corresponding stamps.</p> <p>Whereas vessel curvature previously falsified the assignment of appliqués and models, 3D analysis and visualisation tools now allow a comparison . Metadata created for each object increases the effectiveness and accuracy of determining image context and content. Issues related to the production of the ARS and the process flows within the workshops can be investigated through the analysis of the 3D data.</p> <p>The developed ontology uses CIDOC CRM and various extensions. The data mainly consists of objects (E24), on which e.g. applications (features, E25) can be found. These objects can be described semantically, e.g. by the shape or time epoch. Features are described with observations, e.g. a human type man standing and wearing a beard. These observations lead to interpretations whose arguments can be observations.</p>
Fig 2 in Occurrence Of Dirofilaria Immitis (Nematoda, Onchocercidae) In Red Foxes (Vulpes Vulpes) From The Suburbs Of Kharkiv (Ukraine)
Fig 2. The prevalence of Dirofilaria immitis infection in foxes from separate localities.
Fig 1 in Occurrence Of Dirofilaria Immitis (Nematoda, Onchocercidae) In Red Foxes (Vulpes Vulpes) From The Suburbs Of Kharkiv (Ukraine)
Fig 1. The sites of fox collection in the suburbs of Kharkiv City.
Fig. 2 in Home Ranges Of The Red Fox, Vulpes Vulpes (Carnivora, Canidae) And European Badger, Meles Meles (Carnivora, Mustelidae), In Oak Forests Of Slobozhanshchyna, Ukraine
Fig. 2. Examples of determination the family home range boundaries in 1) foxes and 2) badgers.
Fig. 5 in Home Ranges Of The Red Fox, Vulpes Vulpes (Carnivora, Canidae) And European Badger, Meles Meles (Carnivora, Mustelidae), In Oak Forests Of Slobozhanshchyna, Ukraine
Fig. 5. Fox family home ranges in May–June in 2007-2009 and 2011 in Gomilshanski Lisy NNP.
Fig. 1 in The Amount And Distribution Of The Red Data Book Bird Wetland Species In The Azov-Black Sea Region Of Ukraine According To The Results Of August Counts 2004-2015
Fig. 1. Number of August Counts in the different wetlands of Azov-Black Sea coast of Ukraine.
Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe
Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets.
Advance social information allows red crossbills (Loxia curvirostra) to better conserve body mass and intestinal mass during food stress
<p>Animals prepare for fluctuations in resources through advance storage of energy, planned reduction in energy costs or by moving elsewhere. Unpredictable fluctuations in food, however, may be particularly challenging if animals cannot avoid negative impacts on body condition. Social information may help animals to cope with unpredictable resources if cues from individuals with low foraging success give advance warning about deteriorating conditions. This study investigates the impact of social information on behavior and physiology of food-restricted captive red crossbills (<em>Loxia curvirostra</em>). Birds were restricted to two short feeding periods per day to simulate a decline in resources and were given social information from food-restricted neighbors either before (i.e., predictive) or during (i.e., parallel) the food restriction period. Focal birds better conserved body mass during food restriction if social information was predictive of the decline in resources. Crossbills with predictive information ate more food, had larger intestinal mass and better conserved pectoral muscle size at the end of the restriction period compared to those with parallel social information. These data suggest that birds can use social information to alter behavioral and physiological responses during food shortage in ways that may confer an adaptive advantage for survival.</p>
Data from: Multilevel and sex-specific selection on competitive traits in North American red squirrels.
Individuals often interact more closely with some members of the population (e.g. offspring, siblings or group members) than they do with other individuals. This structuring of interactions can lead to multilevel natural selection, where traits expressed at the group-level influence fitness alongside individual-level traits. Such multilevel selection can alter evolutionary trajectories, yet is rarely quantified in the wild, especially for species that do not interact in clearly demarcated groups. We quantified multilevel natural selection on two traits, postnatal growth rate and birth date, in a population of North American red squirrels (Tamiasciurus hudsonicus). The strongest level of selection was typically within-acoustic social neighbourhoods (within 130m of the nest), where growing faster and being born earlier than nearby litters was key, while selection on growth rate was also apparent both within-litters and within-study areas. Higher population densities increased the strength of selection for earlier breeding, but did not influence selection on growth rates. Females experienced especially strong selection on growth rate at the within-litter level, possibly linked to the biased bequeathal of the maternal territory to daughters. Our results demonstrate the importance of considering multilevel and sex-specific selection in wild species, including those that are territorial and sexually monomorphic.
The non-dereliction in evolution: Trophic specialisation drives convergence in the radiation of red devil spiders (Araneae: Dysderidae) in the Canary Islands
<p>Natural selection plays a key role in deterministic evolution, as clearly illustrated by adaptive radiations. Unlike most spiders, <em>Dysdera</em> species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialisation to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to (1) characterize cheliceral morphologies, (2) unravel their dietary function, (3) examine if they evolved multiple times independently (4) verify whether convergent evolution of morphotypes has occurred and (5) test if specialization could lead to evolutionary irreversibility. We show the existence of nine cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.</p>
The proximity of rapeseed fields influences levels of forest damage by red deer
<p><span>We investigated the relationship between the level of red deer <em>Cervus elaphus</em> bark stripping damage in 68 Norway spruce <em>Picea abies</em> stands, and the presence of rapeseed Brassica napus fields in the surroundings, hypothesising that damage increases with decreasing distance to rapeseed fields. We also considered other potentially influencing factors, such as supplemental feeding, alternative forage availability, and deer use of spruce stands as indexed by a pellet group count.</span></p> <p><span>Bark stripping rates were measured in 68 planted stands of Norway spruce with a minimum size of 1 ha and an age interval of 20-40 years. </span><span>We selected, a priori, stands in forestry plans with a minimum of 80 % spruce. However, all stands were planted even-aged monocultures where cleaning of deciduous species had occurred at younger stages, resulting in a spruce proportion generally close to 100 %. </span><span> In each stand, 10 circular 100 m<sup>2</sup> survey plots were systematically and evenly distributed (with a random starting point). Occurrence of fresh bark-stripping damage (i.e., wounds from preceding winter) was noted for the 10 spruce stems closest to the plot centre (i.e., 100 spruce stems per stand). We measured the distance from the rapeseed fields and feeding stations to the spruce stands by using QGIS. </span></p> <p><span>An index of relative forage availability was measured by estimating percent living vegetation cover of woody browse projected onto the horizontal plane in 20 m2 subplots within targeted stands (the same 10 plots per stand as for the damage survey) and in the surrounding landscape in plots distributed along 500 m transects, one in each of the cardinal directions from the targeted stand (plots distributed at 0, 100, 200, 300, 400, and 500 m from the stand edge (0 m) making a total of 24 transect plots per stand).</span></p> <p><span>The number of red deer pellet groups were counted within targeted spruce stands and in the surrounding landscape to provide indices of relative deer stand usage and overall abundance respectively. Pellet groups were surveyed in 100 m2 circular plots within the stands (the same plots as for damage and forage survey) and in the transect plots used for forage survey described above. Only fresh (from preceding winter) pellet groups were counted.</span></p> <p><span>Spruce stands closer to rapeseed had a significantly higher proportion of damaged stems. The increased level of bark stripping damage was not explained by a higher deer stand use closer to rapeseed fields. Spruce stands closer to supplemental feeding stations had significantly higher damage levels. Damage levels were negatively related to the amount of available browse in the forest. </span></p>
ScienceDex guides
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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.