Find research datasets worth reusing

opencc-by-4.0Jul 2023View details →

Shifting the focus from species to individuals in invasion biology: Individual differences in jumping behaviour

Dataset associated with 'Shifting the focus from species to individuals in invasion biology: Individual differences in jumping behaviour' manuscript.

Raw data containing microsatellite genotypes and otolith microchemistry data for Lutjanus argentiventris individuals from Galapagos (Ecuador) and the Gulf of California (Mexico)

The dataset contains the raw microsatellite genotypes and otolith microchemistry data for yellow snapper (Lutjanus argentiventris) individuals from Galapagos (Ecuador) and the Gulf of California (Mexico), described in the journal publication: Cavole LM, Munguia-Vega A, Miller JA, Salinas-de-Leon P, Marin Jarrin JR, Johnson AF, Laplane ER, Giron-Nava A, Aburto-Oropeza O (2023) Combining otolith chemistry and genetics to infer the population structure of yellow snapper Lutjanus argentiventris. Ecosphere.

Raw data for model implementation examples in paper "Incorporating Detected/Undetected Cooperative and Uncooperative Individuals, and Dynamic Transmission Probabilities in Epidemiological Models"

This dataset contains the historical daily new case numbers referenced in the paper titled "Incorporating Detected/Undetected Cooperative and Uncooperative Individuals, and Dynamic Transmission Probabilities in Epidemiological Models." These numbers were utilized to estimate the basic reproduction number R0 and the aggregated epidemic control measure Kr(t) parameters within the model, as shown in the example implementation section of the paper.

Sensorimotor mechanisms selective to numerosity: evidence from individual differences

This is the dataset related to the article:"Sensorimotor mechanisms selective to numerosity: evidence from individual differences" The file contains subjects Weber Fractions for all of the experiments presented in the paper sub_ID is the participant's identification number

Enrichment of calcium in sea spray aerosol: Insights from bulk measurements and individual particle analysis during the R/V Xuelong cruise in the summertime Ross Sea, Antarctica

This dataset is alout a paper that entiled "Enrichment of calcium in sea spray aerosol: Insights from bulk measurements and individual particle analysis during the R/V Xuelong cruise in the summertime Ross Sea, Antarctica".

Propensity for selfing varies within a population of hermaphroditic snails: coexistence of selfers, outcrossers, and mixed-mating individuals

To understand mating-system evolution in self-compatible hermaphrodites, variation in selfing rates is highly relevant. Empirical studies are rarely designed to capture variation between individuals, instead often comparing species and populations. Yet, evolution primarily occurs within populations, rendering among-individual variation essential. Observed individual selfing rates depend on the environment (e.g., differences in mate availability) and individuals' propensity for selfing. We quantified individual variation in selfing propensity in the snail Radix balthica by conducting laboratory mating trials that manipulated mate availability (low vs. moderate) and estimating selfing rates from progeny arrays. We also measured female lifetime fitness. We found substantial among-individual variation in selfing propensity, including pure selfers (32%), pure outcrossers (31%), and mixed-mating individuals that selfed and outcrossed (37%). Experimental levels of mate availability did not significantly affect selfing rates. Selfers had reduced female liftetime fitness. Our results show that the propensity for selfing can differ considerably among individuals, with similar proportions of selfers, outcrossers, and mixed maters. As mate availability did not affect selfing, our "moderate" level might still have been too low to prompt selfers to outcross. This and the observed fitness differences also cautiously suggest that investigating the heritability of selfing propensities might be worthwhile in this population.

Prediction of Individual Autism Diagnostic Observation Schedule (ADOS) scores based on neural responses during live eye-to-eye contact

Social difficulties are impactful in autism spectrum disorder (ASD), and links between these difficulties and underlying neural processes are active research questions. We present a multivariate classification method for neural data acquired from 36 participants during a live eye-to-eye contact task. Participants were either typically developed (TD) or diagnosed as ASD through gold-standard Autism Diagnostic Observation Schedule (ADOS) evaluation. We hypothesized multivariate classification could discriminate TD vs. ASD based on neural responses. Support vector machine (SVM) classification was able to discriminate between groups during the eye-contact interaction. In addition, it was found that underlying neural patterns contributing to binary classification also predicted measured ADOS scores with high correlation even though ADOS scores were not used for training. The correlation between observed and predicted ADOS scores was 0.72 (p < 0.002) for eye-to-eye contact. These findings suggest neural responses to live eye-to-eye contact are predictive of social symptomatology in ASD.

Associated model data for: Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model

This dataset corresponds to the paper "Size-selective predation effects on juvenile Chinook salmon cohort survival off Central California evaluated with an individual-based model" which is in press at Fisheries Oceanography. The abstract for this paper is as follows: Variation in the recruitment of salmon is often found to be correlated with marine climate indices, but mechanisms behind environment-recruitment relationships remain unclear and correlations often break down over time. We used an ecosystem modeling approach to explore bottom-up and top-down mechanisms linking a variable environment to salmon recruitment variations. Our ecosystem model incorporates a regional ocean circulation sub-model for hydrodynamics, a nutrient-phytoplankton-zooplankton sub-model for producing planktonic prey fields, and an individual-based model (IBM) representing juvenile Chinook salmon (Oncorhynchus tshawytscha), combined with observations of foraging distributions and diet of a seabird predator. The salmon IBM consists of modules, including a juvenile salmon growth module based on temperature and salmon-prey availability, a behavior-based movement module, and a juvenile salmon predation mortality module based on juvenile salmon size distribution and predator-prey interaction probability. Seabird-salmon interactions depend on spatial overlap and juvenile salmon size, whereby salmon that grow past the size range of the prey distribution of the predator will escape predation. We used a 21-year historical simulation to explore interannual variability in juvenile Chinook salmon growth and predation-mediated survival under a range of ocean conditions for sized-based mortality scenarios. We based a series of increasingly complex predation scenarios on seabird observational data to explore variability in predation mortality on juvenile Chinook salmon. We initially included information about the predator spatial distribution, then added population size, and finally, the predator's diet percentage made up of juvenile salmon. Model agreement improves with added predator complexity, especially during periods when predator abundance is high. Overall, our model found that when the fraction of juvenile salmon in seabird diet increased relative to alternate prey (e.g., Northern anchovy Engraulis mordax, and juvenile rockfish Sebastes spp.), there was a concomitant decrease in salmon cohort survival during their first year at sea.

Data from: A hierarchical model for external electrical control of an insect, accounting for inter-individual variation of muscle force properties

Cyborg control of insect movement is promising for developing miniature, high-mobility, and efficient biohybrid robots. However, considering the inter-individual variation of the insect neuromuscular apparatus and its neural control is challenging. We propose a hierarchical model including inter-individual variation of muscle properties of three leg muscles 14 involved in propulsion (retractor coxae), joint stiffness (pro- and retractor coxae), and stance-swing transition (protractor coxae and levator trochanteris) in the stick insect Carausius morosus. To estimate mechanical effects induced by external muscle stimulation, the model is based on the systematic evaluation of joint torques as functions of electrical stimulation parameters. A nearly linear relationship between the stimulus burst duration and generated torque was observed. This stimulus-torque characteristic holds for burst durations of up to 500ms, corresponding to the stance and swing phase durations of medium to fast walking stick insects. Hierarchical Bayesian modeling revealed that linearity of the stimulus-torque characteristic was invariant, with individually varying slopes. Individual prediction of joint torques provides significant benefits for precise cyborg control.

opencc-by-4.0Sep 2023View details →

20230822-IKEM: Intrinsic exploration motivation (individual / social and direct / indirect curiosity, creativity and non-exploration), that influences which object and, if the agent is social, partner(s) are chosen for the interaction, is introduced.

This archive contains the results of a multi-agent simulation experiment [1] carried out with Lazy lavender [2] environment. Experiment Label: 20230822-IKEM Experiment design: Agents interact by playing games with objects and adapt their ontologies to agree on decision taking. Intrinsic exploration motivation (individual / social and direct / indirect curiosity, creativity and non-exploration), that influences which object and, if the agent is social, partner(s) are chosen for the interaction, is introduced. Experiment setting: Agents learn decision trees (transformed into ontologies); choose the objects (and partners) to interact with; adapt by splitting their leaf nodes Hypotheses: 1) Agents will be able to fulfil their motivation in terms of increased exploration (exploratory motivations) and decreased exploration (non-exploratory motivation). 2) Agents with exploratory motivation will be more complete, but less accurate than the baseline and non-exploration. 3) Curious agents will be more accurate and complete, but converge slower in comparison with creativity. 4) In more complex settings (higher number of agents and properties), exploration leads to more completeness, accuracy, distance and faster convergence than the baseline. 5) Agents with non-exploratory motivation will be less accurate and complete than the baseline. 6) The indirect learning models have a higher accuracy and completeness than the direct models. 7) Agents with socially oriented intrinsic motivation will have less diverse knowledge, but agree more and converge faster than agents with individual intrinsic motivation. 8) Heterogeneously motivated agents will have a higher accuracy and completeness, but lower diversity and converge slower than homogeneously motivated agents. Detailed information can be found in index.html or notebook.ipynb. [1] <a href="\">https://sake.re/20230822-IKEM</a> [2] <a href="\">https://gitlab.inria.fr/moex/lazylav/</a>

opencc-zeroOct 2023View details →

Individual survival is dictated by group personality in a marsh ecosystem predator-prey interaction

Predator–prey interactions structure ecological communities, and personality can significantly mediate these interactions. Personality expression is often contingent on social context, suggesting that group personality may be key in determining the outcomes of predator encounters. Here we test the influence of individual personality and group composition on survival of the marsh periwinkle, Littoraria irrorata, when exposed to its main predator, the blue crab, Callinectes sapidus, both integral players in mediating the productivity and health of salt marsh ecosystems. Personality varied along a bold-shy continuum and was unrelated to shell length, though neither trait influenced survival when individual snails were exposed to a predator. However, when snails were partitioned into groups differing in personality composition, snails in groups with bold individuals had higher survival than those in groups with none. While group type did not influence the survival of bold snails, shy snails performed significantly better in mixed groups: the presence of a few bold individuals emerged as especially effective in decreasing mortality of shy snails. The effect of personality on predator escape is thus conditional on group personality composition, indicating that social context can directly impact the survival and success of its individual members, with broad implications for community dynamics.

opencc-by-4.0Oct 2023View details →

Terrestrial laser scanning data of urban trees in Milton Keynes, UK: individual trees and Treegraph outputs

This dataset was used for the analysis of the following publication: Yang, W., Wilkes, P., Vicari, M.B., Hand, K., Calders, K. and Disney, M., 2024. Treegraph: tree architecture from terrestrial laser scanning point clouds. Remote Sensing in Ecology and Conservation. Any use of this dataset should cite the paper above (Creative Commons Attribution NonCommercial License).   ================================================                     Dataset ================================================ TLS_point_clouds: - Data collection: Terrestrial laser scanning data acquired in leaf-off condition in April 2021. - Scanning instrument: We used a RIEGL VZ-400 with a wavelength of 1550 nm, 0.35 mrad beam divergence and 0.04˚ angular resolution. - Locations: The data were collected from three sites in Milton Keynes, UK: Avebury Blvd (Ave), Dansteed Way (Dan), and Overgate (Ove). - File information: Each file is an individual leaf-off tree point cloud in Polygon File Format (.ply), which can be viewed in software such as CloudCompare.   Treegraph_outputs: - Description: Model outputs from Treegraph for individual trees. - File naming convention: [TreeID]-[downsample_voxel_length]-[tip_diameter_if_known].* <ul> <li>*.centres.ply: Skeleton nodes of individual trees.</li> <li>*.mesh.ply: Cylinder model of individual trees.</li> <li>*.json: Geometrical and topological attributes at varying scales, from internode and branch to the whole tree.</li> <li>*.txt: Summary of input parameters, logs of intermediate steps, and a statistical overview of whole-tree structural attributes.</li> </ul>

opencc-by-4.0Oct 2023View details →

DataSet of the study SRM in the median plane with individual and mannequin HRTF

Raw data collected in the study called: "Spatial Release from Masking in the median plane with non-native speakers using individual and mannequin Head Related Transfer Functions".

opencc-by-4.0Oct 2023View details →

IBD segments of previously published Eurasian individuals from "Accurate detection of identity-by-descent segments in human ancient DNA""

IBD segments among 4,248 previously published Eurasian individuals. For details please refer to our manuscript.

opencc-zeroOct 2023View details →

Birth and death dates for individuals of twelve Rhododendron species

Birth (planting) date, depart date, and depart type (C = censored (not dead), D = dead), for individuals of twelve Rhododendron species planted at the Royal Botanic Garden Edinburgh.

opencc-zeroOct 2023View details →

A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants

Underrepresentation of non-European populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72K subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East-Asian-specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell-type-specific effects. We suggest this data set will add to the potential value of Asian precision medicine.

opencc-by-sa-4.0Oct 2023View details →

Data from: Leaf trait variation within individuals mediates the relationship between tree species richness and productivity

This dataset contains tree biometry data and leaf trait data of the Kreinitz Tree Diversity Experiment. In winter 2013/14 and winter 2016/17, height and basal area were measured for all 2880 individuals of the Kreinitz experiment. Tree biometry data is available in the file Data_Kreinitz_Tree.xlsx. In summer 2017, leaf traits for 283 selected trees were measured via near-infrared spectroscopy. For each tree, samples were taken from approximately 3 levels in the trees' crown (total 843 levels). At each level, approximately 4 leaves were harvested (total 3656 leaves) and scanned in triplicates (total 10986 scans). Sampled leaves were scanned on the day of harvest. Leaf trait data is available in the file Data_Kreinitz_Leaf.xlsx.

opencc-byApr 2021View details →

Qasr Hallabat Cistern Individual 4 Ischium

This R ischium fragment was recovered from a cistern within Qasr Hallabat, Jordan and dates to the 8th - 10th centuries AD. 3D modeling and photography of this element was conducted under a permanent loan agreement between the Department of Antiquities of Jordan and East Carolina University. Source: Objaverse 1.0 / Sketchfab