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.
3,788
datasets available to search
ShareScore release 0.9.0
Dataset results
3,788 results for “indices”
The prehistory and early history of the Šumava Mountains (Czech Republic) as seen through anthropogenic pollen indicators and charcoal data
<p>Data for manuscript "<strong>The prehistory and early history of the Šumava Mountains (Czech Republic) as seen through anthropogenic pollen indicators and charcoal data</strong>" by Kozáková R., Bobek P., Dreslerová D., Abraham V. & Svitavská Svobodová H.</p> <p>Data originate from 15 cores in Šumava Mts. (Czech Republic). Original data and further metadata are stored in <a href="https://botany.natur.cuni.cz/palycz/">Czech Quaternary Palynological Database</a>. Data are original pollen counts with original and unified names of all taxa. Stará jímka contains only taxa presented in the paper.</p> <p>See repository <a href="https://github.com/vojtechabraham/PrehistSumavaByAnthropogenIndic">https://github.com/vojtechabraham/PrehistSumavaByAnthropogenIndic</a> for the analysis and plots presented in the paper.</p>
Figure 8 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 8 The intensity of purifying selection of 12 mitochondrial genes of Lateolabrax maculatus. The different colors represent different geographical populations.
Figure 7 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 7 The changed trend of effective population numbers with the time based on Bayesian skyline plot method. X-axis is the timescale before present, and Y-axis is the estimated effective population size. Solid curves indicate median effective population size; the shaded range indicates 95% highest posterior density intervals.
Figure 5 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 5 Bayesian tree constructed based on 86 whole-mitochondrial sequences of Lateolabrax maculatus. Each line represents one individual in the population. The reseda area and orange area represent north population and south population, respectively. Lateolabrax japonicus was used as outgroup.
Figure 6 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 6 The median-joining network constructed based on 78 haplotypes of Lateolabrax maculatus. Each cycle represents a haplotype, the area of the circle is proportional to the frequency of haplotype. Different geographical populations were shown in different colors.
Figure 3 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 3 Plot of pairwise estimates of genetic (FST) and geographical distance between populations of Lateolabrax maculatus.
Figure 4 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 4 Admixture analysis among all populations derived from 85 whole-mitochondrial sequences. The K value was set 2 and 3.
Figure 2 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 2 The structure of Lateolabrax maculatus mitochondrial genome. The total length of mitochondrial genome of L. maculatus was 16,601 bp comprising 13 protein-coding genes (PCGs), 2 rRNA genes and 22 tRNA genes. 249 high-confidence single nucleotide polymorphism (SNP) sites and 24 indels was identified in 85 individuals.
Figure 1 from: Gong J, Chen B, Li B, Zhou Z, Shi Y, Ke Q, Zhang D, Xu P (2020) Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast. Zoologia 37: 1-12. https://doi.org/10.3897/zoologia.37.e49046
Figure 1 Locations of 12 sampling sites of Lateolabrax maculatus. 85 individuals of L. maculatus were collected from 12 geographic locations including Tianjin (TJ), Yantai (YT), Wendeng (WD), Lianyungang (LY), Zhoushan (ZS), Wenzhou (WZ), Shantou (ST), Shenzhen (SZ), Zhanjiang (ZJ), Haikang (HK), Tieshan (TS), Fangcheng (FC) along Chinese coastal waters. The average sea surface temperature (SST) of 1981-2010 at 12 sampling sites were retrieved from NOAA Optimum Interpolation (OI) Sea Surface Temperature (SST) V2 (https://www.esrl.noaa.gov/psd/data/gridded/data.noaa.oisst.v2.html).
GRCm38 (Gencode release 19) indices for snakePipes
<p>Indices for GRCm38 from Gencode release M19 as required by snakePipes.</p>
Stress in the city: meta-analysis indicates no overall evidence for stress in urban vertebrates
<p>As cities continue to grow it is increasingly important to understand the long-term responses of wildlife to urban environments. There have been increased efforts to determine whether urbanization imposes chronic stress on wild animals, but empirical evidence is mixed. Here we conduct a meta-analysis to test whether there is, on average, a detrimental effect of urbanisation based on baseline and stress-induced glucocorticoid levels of wild vertebrates. We found no effect of urbanisation on glucocorticoid levels, and neither sex, season, life stage, taxon, size of the city nor methodology accounted for variation in the observed effect sizes. At face value our results suggest that urban areas are no more stressful for wildlife than rural or non-urban areas, but we offer a few reasons why this conclusion could be premature. We propose that refining methods of data collection will improve our understanding of how urbanization affects the health and survival of wildlife.</p>
Data from: Statin therapy in acute cardioembolic stroke with no guidance-based indication
<p><b>Objective</b> It is uncertain if patients with cardioembolic stroke and absence of a guidance-based indication for statin therapy should be administered a statin for prevention of subsequent vascular events. This study was performed to determine whether the statin therapy is beneficial to prevent major vascular events in this population.</p> <p><b>Methods</b> Using a prospective multicenter stroke registry database, we identified acute cardioembolic stroke patients who were hospitalized between 2008 and 2015. Patients who had other established indications for statin therapy according to current guideline were excluded. Major vascular event was defined as a composite of stroke recurrence, myocardial infarction and vascular death. We performed frailty model analysis with the robust sandwich variance estimator using the stabilized inverse probability of treatment weighting method to estimate hazard ratios of statin therapy on outcomes.</p> <p><b>Results </b>Of 6,124 cardioembolic stroke patients, 2,888 (male, 44.6%; mean age, 75.3 years with 95% confidence interval 74.8-75.8) were eligible; and 1,863 (64.5%) were on statin therapy during hospitalization. After a median follow-up of 359 days, cumulative incidences of major vascular events were 9.3% in the statin users and 20.5% in the non-users (p <0.001 by log-rank test). The adjusted hazard ratios of statin therapy was 0.39 (95% confidence interval, 0.31-0.48) for major vascular events; 0.81 (0.57-1.16) for stroke recurrence; 0.28 (0.21-0.36) for vascular death; and 0.53 (0.45-0.61) for all-cause death, respectively.</p> <p><b>Conclusion</b> Starting statin during acute stage of ischemic stroke may reduce the risk of major vascular events, vascular death and all-cause death in cardioembolic stroke patients with no guidance-based indication for statin.</p>
Biomarker indices and concentrations and biomarker-based temperature estimates from Iberian Margin cores MD99-2331, MD95-2040 and MD95-2042 (160–45 ka BP)
<p>Biomarker metadata and data for cores MD99-2331, MD95-2040, and MD95-2042: depth, age, summed OH-GDGT, iGDGT, and di-unsaturated and tri-unsaturated C<sub>37</sub> alkenone concentrations, OH-GDGT-based, iGDGT-based, and alkenone-based paleothermometric indices, GDGT 2/GDGT-3 ratio, and biomarker-based sea surface temperature (SST) and 0‐ to 200‐m sea temperature (subT; gamma function probability distribution for target temperatures with a = 4.5 and b = 15) estimates. The 1σ analytical uncertainties are 0.008 (0.5 °C) for RI-OH, 0.007 (0.2 °C) for RI-OH′, 0.003 (0.1 °C) for TEX<sub>86</sub>, 0.263 for GDGT-2/GDGT-3, and 0.010 (0.26 °C) for U<sup>K′</sup><sub>37</sub>. RI-OH′-SST estimates are from the following global calibration: SST = (RI-OH′ + 0.029)/0.0422 (Fietz et al., 2020). RI-OH-SST estimates are from the following global calibration: SST = (RI-OH − 1.11)/0.018 (Lü et al., 2015). TEX<sub>86</sub><sup>H</sup>-SST estimates are from the following regional paleocalibration: SST = 68.4 × TEX<sub>86</sub><sup>H</sup> + 33.0 (Darfeuil et al., 2016). U<sup>K′</sup><sub>37</sub>-SST estimates are from the following global calibration: SST = 29.876 × U<sup>K′</sup><sub>37</sub> − 1.334 (Conte et al., 2006). Bayesian calibrations were also used for TEX<sub>86</sub>-SST and TEX<sub>86</sub>-subT estimates (BAYSPAR; Tierney & Tingley, 2014, 2015) and for U<sup>K′</sup><sub>37</sub>-SST estimates (BAYSPLINE; Tierney & Tingley, 2018). Core MD95-2040 U<sup>K′</sup><sub>37</sub> and summed di-unsaturated and tri-unsaturated C<sub>37</sub> alkenone concentration data are from Pailler and Bard (2002). Core MD95-2042 U<sup>K′</sup><sub>37</sub> and summed di-unsaturated and tri-unsaturated C<sub>37</sub> alkenone concentration data covering the 70–45 ka BP period are from Darfeuil et al. (2016). GDGT data for core MD95-2042 samples with TEX<sub>86</sub> values below 0.4 are deemed anomalous and are thus excluded from any description and analysis. Cmbsf, centimeters below sea floor; MIS, marine isotope stage; DO, Dansgaard–Oeschger event; GS, Greenland stadial; H, Heinrich event; GDGT, glycerol dialkyl glycerol tetraether; and N/A, not available.</p>
GRCm38 (Gencode release 19) indices for snakePipes 2.2.0 and later versions
<p>Indices for GRCm38 from Gencode release M19 as required by snakePipes.</p>
GRCh38 (gencode, release 29) indices for snakePipes 2.2.0 and later versions
<p>A human (GRCh38 from Gencode) tarball containing all of the indices needed for snakePipes.</p>
dm6 (ensembl release 94) indices needed by snakePipes 2.2.0 and later versions
<p>Fruit fly indices for snakePipes from Ensembl release 94.</p>
GRCm37/mm9 (Gencode release 1) indices needed by snakePipes 2.2.0 and later versions
<p>Mouse (GRCm37/mm9) indices for snakePipes from Gencode release 1.</p>
Data from: Transcriptional changes during Daphnia pulex development indicate that the maturation decision resembles a rate more than a threshold
Maturation is a critical developmental process, and the age and size at which it occurs have important fitness consequences. Although maturation is remarkably variable, certain mechanisms, including a minimum size or state threshold, are proposed to underlie the process across a broad diversity of taxa. Recent evidence suggests that thresholds may themselves be developmentally plastic, and in the crustacean Daphnia pulex it is unclear whether maturation follows a threshold or is a gradual process more akin to a rate. Changes in gene expression across four instars before and during maturation were compared in a cDNA microarray experiment. Developmental stage was treated statistically both as a discontinuous and a continuous variable, to determine whether genes showed gradual or discrete changes in expression. The continuous analysis identified a greater number of genes with significant differential expression (45) than the discontinuous analysis (11). The majority of genes, including those coding for histones, factors relating to transcription and cell cycle processes, and a putative developmental hormone showed continuous increases or decreases in expression from the first to the fourth instar, suggestive of a prolonged and gradual maturation process. Three genes coding for a fused Vitellogenin/super-oxide dismutase showed increases in expression following the second instar and coincided with the posited maturation threshold, but even their expression increased in a continuous fashion.
Data from: Meta-analysis indicates that oxidative stress is both a constraint on and a cost of growth
Oxidative stress (OS) as a proximate mechanism for life-history trade-offs is widespread in the literature. One such resource allocation trade-off involves growth rate, and theory suggests that OS might act as both a constraint on and a cost of growth, yet studies investigating this have produced conflicting results. Here, we use meta-analysis to investigate whether increased OS levels impact on growth (OS as a constraint on growth) and whether greater growth rates can increase OS (OS as a cost of growth). The role of OS as a constraint on growth was supported by the meta-analysis. Greater OS, in terms of either increased damage or reduced levels of antioxidants, was associated with reduced growth although the effect depended on the experimental manipulation used. Our results also support an oxidative cost of growth, at least in terms of increased oxidative damage, although faster growth was not associated with a change in antioxidant levels. These findings that OS can act as a constraint on growth support theoretical links between OS and animal life histories and provide evidence for a growth–self-maintenance trade-off. Furthermore, the apparent oxidative costs of growth imply individuals cannot alter this trade-off when faced with enhanced growth. We offer a starting platform for future research and recommend the use of oxidative damage biomarkers in nonlethal tissue to investigate the growth–OS relationship further.
Data from: Phenotypic variation and covariation indicate high evolvability of acoustic communication in crickets
Studying the genetic architecture of sexual traits provides insight into the rate and direction at which traits can respond to selection. Traits associated with few loci and limited genetic and phenotypic constraints tend to evolve at high rates typically observed for secondary sexual characters. Here, we examined the genetic architecture of song traits and female song preferences in the field crickets Gryllus rubens and G. texensis. Song and preference data were collected from both species and interspecific F1 and F2 hybrids. We first analysed phenotypic variation to examine interspecific differentiation and trait distributions in parental and hybrid generations. Then, the relative contribution of additive and additive-dominance variation was estimated. Finally, phenotypic variance-covariance (P) matrices were estimated to evaluate the multivariate phenotype available for selection. Song traits and preferences had unimodal trait distributions and hybrid offspring were intermediate with respect to the parents. We uncovered additive and dominance variation in song traits and preferences. For two song traits we found evidence for X-linked inheritance. On one hand, the observed genetic architecture does not suggest rapid divergence, although sex-linkage may have allowed for somewhat higher evolutionary rates. On the other hand, P matrices revealed that multivariate variation in song traits aligned with major dimensions in song preferences, suggesting a strong selection response. We also found strong covariance between the main traits that are sexually selected and traits that are not directly selected by females, providing an explanation for the striking multivariate divergence in male calling songs despite limited divergence in female preferences.
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.