Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
617
datasets available to search
ShareScore release 0.9.0
Dataset results
617 results for “base population”
Dopamine axon population Ca signals in the striatum during odor cue- and reward-based choice tasks in mice
Open the record for dataset details and reuse information.
Data from: Evaluating the existence and benefit of major histocompatibility complex-based mate choice in an isolated owl population
Open the record for dataset details and reuse information.
Data from: Climate-based seed transfer of a widespread shrub: population shifts, restoration strategies and the trailing edge
Open the record for dataset details and reuse information.
Data from: Conservation action based on threatened species capture taxonomic and phylogenetic richness in breeding and wintering populations of Central Asian birds
Open the record for dataset details and reuse information.
Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies
Open the record for dataset details and reuse information.
Data from: Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population
Open the record for dataset details and reuse information.
Code from: A theoretical framework for trait-based eco-evolutionary dynamics: population structure, intraspecific variation, and community assembly
Open the record for dataset details and reuse information.
Data from: Coverage of the 2011 Q fever vaccination campaign in the Netherlands, using retrospective population-based prevalence estimation of cardiovascular risk-conditions for chronic Q fever
Open the record for dataset details and reuse information.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Open the record for dataset details and reuse information.
Data from: A trait-based approach to predict population genetic structure in bees
Open the record for dataset details and reuse information.
Data from: Risk factors for bloodborne viral hepatitis in healthcare workers of Pakistan: a population based case–control study
Open the record for dataset details and reuse information.
Supplemental material from: A population-based prevalence of myotonic dystrophy type 1
Open the record for dataset details and reuse information.
Differential influence of Slc7a11 expression and body condition on pheomelanin‐based pigmentation in two Eurasian nuthatch Sitta europaea populations with different predation risk
Open the record for dataset details and reuse information.
Sex prediction based on teeth mesiodistal width: model development in a Portuguese population
<p>168 pretreatment dental casts of orthodontics Portuguese subjects (59 males and 109 females) were included. Mesiodistal widths from right first molar to left first molar were measured on each pretreatment cast to the nearest 0.01 mm using digital caliper.</p>
Code for Individual Based Model to assess impact of KHV release on carp population
<p><b>1: </b>Common carp (<i>Cyprinus carpio</i>) is one of the top global invasive vertebrates and can cause significant ecological damage. The Australian Government's National Carp Control Program (NCCP) proposes to release Koi Herpesvirus (KHV) to eradicate feral carp in one of the largest ecological interventions ever attempted. Ecological and human health risks have been highlighted regarding the release of a highly pathogenic viral biocontrol for an aquatic species. The efficacy of KHV has also been questioned, and it has not been demonstrated to produce lasting population reductions.</p> <p> </p> <p>2. We developed an individual-based model (IBM) to examine the ecological and evolutionary response of a carp population after KHV release. This simulated the interaction between fish life history, viral epidemiology, host genetic resistance and population demography to critically evaluate the impact of KHV release under optimal conditions and a "best case scenario" for disease transmission.</p> <p> </p> <p>3. KHV will rarely result in prolonged reductions or population extinctions. Crucially, realistic scenarios result in a rapidly rebounding population of resistant individuals. Additional measures aimed to reduce carp population recovery rate (e.g. with genetic engineering) require rapid efficacy to significantly reduce carp numbers alongside KHV.<br> </p> <p>4. Fish fecundity has an overwhelming influence on viral efficacy as a biocontrol agent when combined with genetic resistance within a population. A high probability of population extinction is only met when carp fecundity is reduced to 1% of biological observations.<br> </p> <p><span>5.<i> Synthesis and applications. </i></span>We use an individual-based model to evaluate the efficacy of Koi Herpesvirus biocontrol in Common <a>Ca</a>rp, and find that high host fecundity combined with genetic resistance results in rapid population rebound after initial large fish-kills. Biocontrol approaches relying on natural selection lose efficacy over successive generations as resistance genes increases in frequency. Given the intense logistical effort and risks to ecosystems and human health associated with large fish kills after viral release, we suggest that sustained manual removal, alongside ecological restoration to favour recovery of native species, provides a risk-free approach to reducing populations.<br> </p>
Data from: Estimating population density of insectivorous bats based on stationary acoustic detectors: a case study
<p>1. Automated recording units are commonly used by consultants to assess environmental impacts and to monitor animal populations. Although estimating population density of bats using stationary acoustic detectors is key for evaluating environmental impacts, estimating densities from call activity data is only possible through recently developed numerical methods, as the recognition of calling individuals is impossible.<br> 2. We tested the applicability of generalized random encounter models (gREMs) for determining population densities of three bat species (Common pipistrelle <em>Pipistrellus pipistrellus</em>, Northern bat Eptesicus nilssonii,, and Natterer's bat Myotis nattereri) based on passively collected acoustical data. To validate the results, we compared them to (i) density estimates from the literature and to (ii) Royle-Nichols (RN) models of detection/non-detection data.<br> 3. Our estimates for M. nattereri matched both the published data and RN-model results. For E. nilssonii, the gREM yielded similar estimates to the RN-models, but the published estimates were more than twice as high. This discrepancy might be because the high-altitude flight of E. nilssonii is not accounted for in gREMs. Results of gREMs for P. pipistrellus were supported by published data but were approximately 10 times higher than those of RN-models. RN-models use detection/non-detection data and this loss of information probably affected population estimates of very active species like P. pipistrellus.<br> 4. gREM models provided realistic estimates of bat population densities based on automatically recorded call activity data. However, the average flight altitude of species should be accounted for in future analyses. We suggest including flight altitude in the calculation of the detection range to assess the detection sphere more accurately and to obtain more precise density estimates.</p>
Data from: Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes
In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of the updated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep.
Data from: Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting
Objective: We explored genetic and lifestyle risk factors of MRI-defined brain infarcts (BI) in large population-based cohorts. Methods: We performed meta-analyses of genome-wide association studies (GWAS) and examined associations of vascular risk factors and their genetic risk scores (GRS) with MRI-defined BI and a subset of BI, namely small sub-cortical BI (SSBI), in eighteen population-based cohorts (N=20,949) from five ethnicities (3,726 with BI, 2,021 with SSBI). Top loci were followed up in seven population-based cohorts (N=6,862, 1,483 with BI, 630 with SBBI), and tested associations with related phenotypes including ischemic stroke and pathologically-defined BI. Results: The mean prevalence was 17.7% for BI and 10.5% for SSBI, steeply rising after age 65. Two loci showed genome-wide significant association with BI: FBN2, P=1.77×10-8 and LINC00539/ZDHHC20, P=5.82×10-9. Both have been associated with blood pressure (BP) related phenotypes, but did not replicate in the smaller follow-up sample nor show associations with related phenotypes. Age and sex-adjusted associations with BI and SSBI were observed for BP traits (P-value for BI, P[BI]=9.38×10-25; P[SSBI]=5.23×10-14 for hypertension), smoking (P[BI]=4.4×10-10; P[SSBI]=1.2×10-4), diabetes (P[BI]=1.7×10-8; P[SSBI]=2.8×10-3), previous cardiovascular disease (P[BI]=1.0×10-18; P[SSBI]=2.3×10-7), stroke (P[BI]=3.9×10-69; P[SSBI]=3.2×10-24), and MRI-defined white matter hyperintensity burden (P[BI]=1.43×10-157; P[SSBI]=3.16×10-106), but not with body-mass-index or cholesterol. GRS of BP traits were associated with BI and SSBI (P≤0.0022), without indication of directional pleiotropy. Conclusions: In this multi-ethnic GWAS meta-analysis, including over 20,000 population-based participants, we identified genetic risk loci for BI requiring validation once additional large datasets become available. High BP, including genetically determined, was the most significant modifiable, causal risk factor for BI.
Data from: Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2–6 and identification of five novel MICB alleles
The polymorphism of major histocompatibility complex class I chain-related gene B (MICB) and variations in MICB alleles in a variety of populations have been characterized using several genotyping approaches. In the present study, a novel polymerase chain reaction sequence-based typing (PCR-SBT) method was established for the genotyping of MICB exons 2–6, and the allelic frequency of MICB in the Zhejiang Han population was investigated. Among 400 unrelated healthy Han individuals from Zhejiang Province, China, a total of 20 MICB alleles were identified, of which MICB*005:02:01, MICB*002:01:01, and MICB*004:01:01 were the most predominant alleles, with frequencies of 0.57375, 0.1225, and 0.08375, respectively. Nine MICB alleles were detected on only one occasion, giving a frequency of 0.00125. Of the 118 distinct MICB ∼ HLA-B haplotypes identified, 42 showed significant linkage disequilibrium (P < 0.05). Haplotypes MICB*005:02:01 ∼ B*46:01, MICB*005:02:01 ∼ B*40:01, and MICB*008 ∼ B*58:01 were the most common haplotypes, with frequencies of 0.0978, 0.0761, and 0.0616, respectively. Five novel alleles, MICB*005:07, MICB*005:08, MICB*027, MICB*028, and MICB*029 were identified. Compared with the MICB*005:02:01 sequence, a G > A substitution was observed at nucleotide position 210 in MICB*005:07, and a 1,134 T > C substitution in MICB*005:08 and an 862 G > A substitution in MICB*027 were detected. In addition, it appears that MICB*028 probably arose from MICB*004:01:01 with an A to G substitution at position 1,147 in exon 6. MICB*029 had a G > T transversion at nucleotide position 730 in exon 4, compared with that of MICB*002:01:01. On the basis of the new PCR-SBT assay, these observed results demonstrated MICB allelic variations in the Zhejiang Han population.
Data from: Incidence rate of community-acquired pneumonia in adults: a population-based prospective active surveillance study in three cities in South America
OBJECTIVE: To determine the incidence rate and mortality of community-acquired pneumonia (CAP) in adults in three cities in Latin America during a three-year period. DESIGN: Prospective population based study. SETTING: Healthcare facilities (outpatient centers and hospitals) in the cities of General Roca (Argentina), Rivera (Uruguay) and Concepcion (Paraguay). PARTICIPANTS: 2302 adults aged 18 years and older with CAP were prospectively enrolled between January 2012 and March 2015. MAIN OUTCOME MEASURES: Incidence rate of CAP in adults, predisposing conditions for disease, mortality at 14 days and at one year were estimated. Incidence rate of CAP, within each age group, was calculated by dividing the number of cases by the person-years of disease-free exposure time based on the last census; incidence rates were expressed per 1000 person-years. RESULTS: Median age of participants was 66 years, 46.44 % were men, 68% were hospitalized. Annual incidence rate was 7.03 (CI95% 6.64-7.44) per 1000 person-years in General Roca, 6.33 (CI95% 5.92-6.78) per 1000 person-years in Rivera and 1.76 (CI95% 1.55-2.00) per 1000 person-years in Concepcion. Incidence rates were highest in participants aged over 65 years. 82.4% had at least one predisposing condition and 48% had 2 or more (multi-morbidity). Chronic heart disease (43.6%) and smoking (37.3%) were the most common risk factors. 14-day mortality rate was 12.1% and one-year mortality was 24.9%. Multi-morbidity was associated with an increased risk of death at 14 days (OR 2.91; 2.23 to 3.80) and at 1 year (OR 3.00; 2.44 to 3.70). CONCLUSIONS: We found a high incidence rate of CAP in adults, ranging from 1.76 to 7.03 per 1000 person-years, in three cities in South America, disclosing the high burden of disease in the region. Efforts to improve prevention strategies are needed.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.