Find research datasets worth reusing

opencc-by-4.0Feb 2023View details →

Audio files and dataset: Guess who? Evaluating individual acoustic monitoring for males and females of the Tawny Pipit, a migratory passerine bird with a simple song

We have uploaded the audio files (song files + recording files) and the dataset of the analysis conducted in our manuscript entitled ''Guess who? Evaluating individual acoustic monitoring for males and females of the Tawny Pipit, a migratory passerine bird with a simple song''. This study is published in the scientific journal ''Journal of Ornithology''. We have also provided a txt. file, called 'Read me' explaining the uploaded data in more detail.

opencc-by-4.0Feb 2023View details →

Photo - Identification of individuals of Atlantic salmon (eye dataset)

Identification of individuals of salmon. Eye data. Original and processed data of four datasets. Totally 330 fish were collecred for the short term scenario and 30 out of 330 fish were tagged and kept for a long term experiment.

opencc-by-4.0Jan 2023View details →

Non - invasive identication of individuals of European seabass Dicentrarchus labrax (short term)

The precision fish farming concept has been widely investigated in research and is highly desirable in aquaculture because it creates opportunities for precisely controlling and monitoring fish cultivation processes and increasing fish welfare. The automatic identification of individual fish could be one of the keys to enabling individual fish treatment. In a previous study, we already demonstrated that the visible patterns on a fish’s body can be used for the non-invasive individual identification of fishes from the same species (with obvious skin patterns, such as salmonids) over long-term periods. The aim of this study was to verify the possibility of using fully-automatic non-invasive photo-identification of individual fish based on natural marks on the fish’s body without any obvious skin patterns. This approach is an alternative to stressful invasive tagging and marking techniques. Scale patterns on the body and operculum, as well as lateral line shapes, were used as discriminative features for the identification of individuals in a closed group of fish. We used the European seabass Dicentrarchus labrax. The identification method was tested on  two separate short-term data sets (pattern variability test) and two long-term data sets (pattern stability test) for European seabass (300 individual fish). The accuracy of classification was 100% for both the short-term and long-term experiments. According to these results, the methods used for automatic non-invasive image-based individual-fish identification can also be used for fish species without obvious skin patterns.

opencc-by-4.0Feb 2023View details →

Non - invasive identification of individuals of Atlantic salmon (aquarium data)

Non - invasive identification of individuals of Atlantic salmon (aquarium data). There are four datasets. First dataset is a 330 fish individuals of atlantic Salmon, they are separated ito 6 part. Then, other Three datsets are tagged 30 fish out of those 330 fish. There are original data and processed data. data were collected in aquarium with water.

opencc-by-4.0Mar 2023View details →

Non-invasive identification of individuals of Atlantic salmon (tent data)

Non-invasive identification of individuals of Atlantic salmon (tent data). 328 fish were sampled. 30 fish were tagged for next data collection. totally 4 data collection were done. The fish were photographed in tent out of water. The fish were photographed on the green background for simple fish localization. Each image was processed separately. First the green background was detected based on the defined value of the green in HSV color space. The backgound was used as the area of fish appearance. In the secodn step the fish was segmented on the background using the specific color of the fish in HSV color space. The fish was detected as the largest object. Some morphological operations were used to correct fish shape. The object was rotated to the horizontal position. The fish tail was removed by the algorithm because it was detected on some images and not detected on the rest. Therefore the algorithm detects the begining of back tail as the most narrow place at back part of the fish. The lenght of the fish and the height of the fish was used for the localization of the ROI. The ROI is shown on the image bellow. The ROI was selected to cover the fish body with most visible patter. Uploaded files - original and processd files for all data collections.

Data for: Phenotypic plasticity increases exposure to extreme climatic events that reduce individual fitness

Climate models, and empirical observations, suggest that anthropogenic climate change is leading to changes in the occurrence and severity of extreme climatic events (ECEs). Effects of changes in mean climate on phenology, movement, and demography in animal and plant populations are well documented. In contrast, work exploring the impacts of ECEs on natural populations is less common, at least partially due to the challenges of obtaining sufficient data to study such rare events. Here, we assess the effect of changes in ECE patterns in a long-term study of great tits, near Oxford, over a 56-year period between 1965 and 2020. We document marked changes in the frequency of temperature ECEs, with cold ECEs being twice as frequent in the 1960s than at present, and hot ECEs being ~three times more frequent between 2010 and 2020 than in the 1960s. While the effect of single ECEs was generally quite small, we show that increased exposure to ECEs often reduces reproductive output, and that in some cases, the effect of different types of ECE is synergistic. We further show that long-term temporal changes in phenology, resulting from phenotypic plasticity, lead to an elevated risk of exposure to low-temperature ECEs early in reproduction, and hence suggest that changes in ECE exposure may act as a cost of plasticity. Overall, our analyses reveal a complex set of risks of exposure and effects as ECE patterns change and highlight the importance of considering responses to changes in both mean climate and extreme events. Patterns in exposure and effects of ECEs on natural populations remain underexplored and continued work will be vital to establish the impacts of ECEs on populations in a changing climate.

opencc-by-4.0Dec 2021View details →

Data for: Neural correlates of individual odor preference in Drosophila

Data associated with: Neural correlates of individual odor preference in Drosophila Behavior varies even among genetically identical animals raised in the same environment. However, little is known about the circuit or anatomical origins of this individuality. We show individual Drosophila odor preferences (odor-vs-air and odor-vs-odor) are predicted by idiosyncratic calcium dynamics in olfactory receptor neurons (ORNs) and projection neurons (PNs), respectively. Variation in ORN presynaptic density also predicts odor-vs-odor preference. The ORN-PN synapse appears to be a locus of individuality where microscale variation gives rise to idiosyncratic behavior. Finally, simulating microscale stochasticity in ORN-PN synapses of a 3,062-neuron model of the antennal lobe recapitulates patterns of variation in PN calcium responses matching experiments. Our results demonstrate how physiological and microscale structural circuit variations can give rise to individual behavior, even when genetics and environment are held constant.

Stronger effect of individual species' traits than shading on aquatic plant community productivity and interspecific competition

Competition is one of the major factors structuring plant communities. Species with similar traits generally compete more intensely and have more similar yield than functionally dissimilar species, which often respond differently to environmental change. Little is known about how the interacting species' traits influence the effect of environmental change on interspecific competition. However, theory predicts that environmental change should lead to more asymmetric competition, by favouring the species best adapted to the particular environmental change. Here we used a mesocosm experiment with three common aquatic plant species from the Baltic Sea (Northern Europe), to test how community productivity and competition asymmetry were affected by functional dissimilarity, individual species' traits, and a common stressor: shading. Competition asymmetry was defined as the absolute difference in reductions in yield relative to monocultures of two interacting species. Community productivity decreased and competition asymmetry increased with functional dissimilarity of the interacting species, possibly explained by the traits of the superior species, which had higher specific leaf area, maximum canopy height, and primary production rate than the subordinate species. Community productivity was not affected by shading, contrary to our expectation, while competition asymmetry was higher in shaded than ambient conditions. Individual species yield depended on species identity and species combination. Only the shortest species was negatively affected by shading. Thus, by favouring tall-growing species, shading can alter interspecific competition. Together, these findings suggest that non-random species loss following environmental change can be caused by competitive exclusion, in addition to a direct effect of abiotic filtering.

Open-population SCR model to estimate spatiotemporal variation in individual birth locations, detection rates, and survival

This is an open population SCR model developed by R. Chandler and K. Engebretsen. The full model incorporates 4 spatial covariates in birth location density submodel, 3 location-specific, temporal covariates in the detection submodel, and 4 spatial covariates in the survival submodel. Formatted data is provided for the 2015 and 2016 fawning season in south Florida and the model can be fit using the script fitFawnModel.R.

Data from: Mitochondrial function declines with age within individuals but is not linked to the pattern of growth or mortality risk in zebra finch

Mitochondrial dysfunction is considered a highly conserved hallmark of ageing. However, most studies in both model and non-model organisms are cross-sectional in design; therefore, little is known, at the individual level, on how mitochondrial function changes with age, its link to early developmental conditions or its relationship with survival. Here we manipulated the postnatal growth in zebra finches (Taeniopygia guttata) via dietary modification that induced accelerated growth without changing adult body size. In the same individuals, we examined blood cells mitochondrial functioning (mainly erythrocytes) when they were young (ca 36 weeks) and again in mid-aged (ca 91 weeks) adulthood. Mitochondrial function was strongly influenced by age but not by postnatal growth conditions. Across all groups, within individual ROUTINE respiration, OXPHOS and OXPHOS coupling efficiency significantly declined with age, while LEAK respiration increased. However, we found no link between mitochondrial function and the probability of survival into relatively old age (ca 4 years). Our results suggests that the association between accelerated growth and reduced longevity, evident in this as in other species, is not attributable to age-related changes in any of the measured mitochondrial function traits.

opencc-by-4.0Mar 2023View details →

Risk factors that modifies the familial aggregation of the cervix-uterine cancer in affected individuals

Base de datos

opencc-zeroApr 2023View details →

Data for: Evaluation of antibody kinetics and durability in health individuals vaccinated with inactivated COVID-19 vaccine (CoronaVac): a cross-sectional and cohort study in Zhejiang, China

Background: Although inactivated COVID-19 vaccines are proven to be safe and effective in the general population, the dynamic response and duration of antibodies after vaccination in the real world should be further assessed. Methods: We enrolled 1067 volunteers who had been vaccinated with one or two doses of CoronaVac in Zhejiang Province, China. Another 90 healthy adults without previous vaccinations were recruited and vaccinated with three doses of CoronaVac, 28 days and 6 months apart. Serum samples were collected from multiple timepoints and analyzed for specific IgM/IgG and neutralizing antibodies (NAbs) for immunogenicity evaluation. Antibody responses to the Delta and Omicron variants were measured by pseudovirus-based neutralization tests. Results: Our results revealed that binding antibody IgM peaked 14–28 days after one dose of CoronaVac, while IgG and NAbs peaked approximately 1 month after the second dose and then declined slightly over time. Antibody responses had waned by month 6 after vaccination and became undetectable in the majority of individuals at 12 months. Levels of NAbs to live SARS-CoV-2 were correlated with anti-SARS-CoV-2 IgG and NAbs to pseudovirus, but not IgM. Homologous booster around 6 months after primary vaccination activated anamnestic immunity and raised NAbs 25.5-fold. The neutralized fraction subsequently rose to 36.0% for Delta (p=0.03) and 4.3% for Omicron (p=0.004), and the response rate for Omicron rose from 7.9% (7/89) to 17.8% (16/90). Conclusions: Two doses of CoronaVac vaccine resulted in limited protection over a short duration. The inactivated vaccine booster can reverse the decrease of antibody levels to prime strain, but it does not elicit potent neutralization against Omicron; therefore, the optimization of booster procedures is vital.

opencc-zeroApr 2023View details →

Hurricanes affect diversification among individual life courses of a primate population

<ol> <li>Extreme climatic events may influence individual-level variability in phenotypes, survival, and reproduction, and thereby drive the pace of evolution. Climate models predict increases in the frequency of intense hurricanes, but no study has measured their impact on individual life courses within animal populations.</li> <li>We used 45 years of demographic data of rhesus macaques to quantify the influence of major hurricanes on reproductive life courses using multiple metrics of dynamic heterogeneity accounting for life course variability and life history trait variances.</li> <li>To reduce intraspecific competition, individuals may explore new reproductive stages during years of major hurricanes, resulting in higher temporal variation in reproductive trajectories. Alternatively, individuals may opt for a single optimal life history strategy due to trade-offs between survival and reproduction.</li> <li>Our results show that heterogeneity in reproductive life courses increased by 4% during years of major hurricanes, despite a 2% reduction in the asymptotic growth rate due to an average decrease in mean fertility and survival, i.e. shortened life courses and reduced reproductive output. In agreement with this, the population is expected to achieve stable population dynamics faster after being perturbed by a hurricane (ρ = 1.512; 95% CI: 1.488, 1.538), relative to ordinary years (ρ = 1.482;1.475,1.490).</li> <li>Our work suggests that natural disasters force individuals into new demographic roles to potentially reduce competition during unfavorable environments where mean reproduction and survival are compromised. Variance in lifetime reproductive success and longevity are differently affected by hurricanes, and such variability is mostly driven by survival. </li> </ol>

opencc-zeroApr 2023View details →

Model for: Characterizing long‐term population conditions of the elusive red tree vole with dynamic individual‐based modeling

<div class="abstract"> Old growth forests are declining globally, threatening dependent wildlife. Many arboreal old‐growth obligates, such as the threatened red tree vole, are difficult to monitor for changes in habitat occupancy, and abundance. Yet, conservation planning relies on this information to prevent population declines. We integrated a range of species, habitat, and landscape change information to develop a dynamic habitat‐population model. The spatial individual‐based model simulated dynamic patterns of occupancy that responded to annual habitat maps, describing 36 years of observed change. We simulated population dynamics and local movement to characterize changes in occupancy and abundance, and the capacity of remaining habitat to support red tree voles. Red tree vole redistribution patterns strongly corresponded to wildfire footprints and timber extraction locations. Population strongholds are likely to exist in clumped pockets of old‐growth forest that were unaffected by wildfire and in protected old forest reserves. However, the exact number and locations of local clusters remain uncertain. Simulated population losses occurred at different paces in different places, underscoring the need for recurring evaluation of population changes with field occupancy surveys and modeled evaluations that can anticipate potential connectivity and extirpation thresholds. This modeling approach was effective at leveraging existing information for a data‐light species to assess how historical changes to the quantity, quality, and configuration of habitat likely influenced the potential landscape capacity, species abundance, and distribution. Dynamic individual‐based modeling can benefit conservation planning for red tree vole and other reclusive forest species by providing biologically nuanced assessments of abundance and distribution. Such models can also project the long‐term benefits and impacts of spatially explicit land management plans. </div> <div class="abstract"></div>

Individual-plant selectivity by sheep in drylands scales-up at plant population level and controls the forage supply and its accessibility

Diet selectivity by domestic herbivores controls plant community structure and dynamics and may induce rangeland degradation, particularly in drylands. However, management decisions frequently ignore herbivore selectivity. Here, we studied how grass morphology controls sheep selectivity for individual plants, and how this selectivity interacts with grazing intensity to determine population plant-size distributions and the forage supply. In Patagonian steppes, we manipulated the plant morphology (size and standing-dead proportion) of three dominant grass species differentially preferred by sheep for four years. Then, we evaluated how these morphological alterations affected intra- and inter-specific preference patterns. We also evaluated how grazing intensity (ungrazed, moderate grazing, and intensive grazing) affected the plant-size distribution of the three species, the forage supply, and its accessibility. For the highly preferred species, herbivores selected plants that were either naturally or experimentally short, with low proportion of standing-dead biomass. In contrast, morphological changes did not alter the within-species selectivity of the least preferred species. Grazing intensity strongly changed the population plant-size distribution of preferred species in ways that resembled the experimental manipulations of morphology. Moderate grazing showed the greatest morphological heterogeneity among individuals. When integrating the green biomass of forage species' individuals at ecosystem level, we found that the forage supply was the highest in ungrazed sites and decreased as grazing intensity increased. However, considering the dissuading effect of the standing-dead proportion of plants, the accessible forage was the highest under moderate grazing. Synthesis and applications. Our findings (i) showed that, within preferred species, sheep selectivity at individual-plant level is controlled by morphological characteristics that determine accessibility to green high-quality biomass. This effect was as important as that of species identity; (ii) empirically proved plant-animal positive feedback at individual level; and (iii) revealed how the individual-plant selectivity scales-up at population level and controls the forage supply, but also its accessibility. Our complementary approach generates critical knowledge for developing management practices to control key forage species defoliation and to adjust the grazing pressure to the offer of accessible forage, avoiding the common carrying capacity overestimation. These aspects are essential for sustainable production in grazed drylands.

Climatic forcing and individual heterogeneity in a resident mountain bird: legacy data reveal effects on reproductive strategies

Optimization of clutch size and timing of reproduction have substantial effects on lifetime reproductive success in vertebrates, and both individual quality and environmental variation may impact life history strategies. We tested hypotheses related to maternal investment and timing of reproduction, using 17 years (1978-1994) of individual-based life history data on willow ptarmigan (Lagopus l. lagopus, n=290 breeding females with n=319 breeding attempts) in central Norway. We analysed whether climatic variation and individual state variables (age and body mass) affected number of offspring and timing of reproduction, and individual repeatability in strategies. The results suggest that willow ptarmigan share a common optimal clutch size that is largely independent of measured individual states. While we found no clear direct weather effects on clutch size, higher spring temperatures advanced onset of breeding, and early breeding was followed by an increased number of offspring. Warmer springs were positively related to maternal mass, and mass interacted with clutch size in production of hatchlings. Finally, clutch size and timing of reproduction were highly repeatable within individuals, indicating that individual quality guided trade-offs in reproductive effort. Our results demonstrate how climatic forcing and individual heterogeneity in combination influenced life history traits in a resident montane keystone species.

opencc-by-4.0May 2023View details →

Tailored machine learning for evaluating the long-term diabetes risk in older individuals: Findings from The Irish Longitudinal Study on Ageing (TILDA)

The original data for "Tailored machine learning for evaluating the long-term diabetes risk in older individuals: Findings from The Irish Longitudinal Study on Ageing (TILDA)" that published in BMJ Open.

Data from: Community-level canopy reflectance in grazed grasslands is linked to the habitat preferences of individual plant species

Spectral remote sensing provides tools for biological monitoring and can be used to characterize habitat quality in grasslands. These data have been used to study the relationships between plant community composition and remotely sensed canopy reflectance in grazed grasslands. The study area is located on the island of Öland, Sweden, and the data were collected in grazed grasslands that represent a succession from previously arable fields to old semi-natural pastures. All included grassland sites have been assigned to three different classes of grassland age, defined by the grazing continuity in years: young (5–14 years), intermediate-aged (15–49 years), and old (>50 years). The plant community data consist of presences/absences for 100 vascular plant species in 104 (4 m × 4 m) sample plots positioned in open grassland vegetation. Information on species' habitat preferences is included and has been used to explain the associations between plant species' occurrences and the variation in community-level canopy reflectance. The remote sensing data consist of 317 hyperspectral bands in the wavelength regions 414–1322 nm, 1496–1797 nm, and 2050–2351 nm, and show the mean reflectance in each spectral band for the 104 sample plots. The main gradient in the hyperspectral data is characterized by contrasting reflectance values between bands located in the NIR spectra and bands located in the red, blue, and SWIR spectra. Grassland canopy reflectance was able to explain variation in the occurrences of individual plant species, particularly those with distinct habitat preferences. Species' habitat preferences indicated that vegetation reflectance in the red, blue, SWIR, and NIR spectra was linked to the plant-availability of mineral nitrogen. In contrast, species' phosphorus preferences showed stronger associations with reflectance in the green and red-edge spectra.

Data from: Maintenance and expansion of genetic and trait variation following domestication in a clonal crop: Enset tGBS individual genotype data

Clonal propagation enables favourable crop genotypes to be rapidly selected and multiplied. However, the absence of sexual propagation can lead to low genetic diversity and accumulation of deleterious mutations, which may eventually render crops less resilient to pathogens or environmental change. To better understand this trade-off, we characterise the domestication and contemporary genetic diversity of Enset (Ensete ventricosum), an indigenous African relative of bananas (Musa) and principal starch staple for 20 million Ethiopians. Wild enset is strictly sexually outcrossing, but in cultivation is propagated clonally and associated with diversification and specialisation into hundreds of named landraces. We applied tGBS sequencing to generate genome-wide genotypes for 192 accessions from across enset's cultivated distribution, and surveyed 1340 farmers on enset agronomic traits. Overall, reduced heterozygosity in the domesticated lineage was consistent with a domestication bottleneck that retained 37% of wild diversity. However, an excess of putatively deleterious missense mutations at low frequency present as heterozygotes suggested accumulation of mutational load in clonal domesticated lineages. Our evidence indicates that the major domesticated lineages initially arose through historic sexual recombination associated with a domestication bottleneck, followed by amplification of favourable genotypes through an extended period of clonal propagation. Among domesticated lineages we found significant phylogenetic signal for multiple farmer-identified food, nutrition and disease resistance traits and little evidence of contemporary recombination. Development of future-climate adapted genotypes may require crop breeding, but outcrossing risks exposing deleterious alleles as homozygotes. This trade-off may partly explain the ubiquity and persistence of clonal propagation over recent centuries of comparative climate stability.