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9,786 results for “selection”
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome
<p><br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.</p> <p>1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts</p> <p>5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups </p> <p>6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.</p> <p>7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2.</p> <p>8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.</p> <p>9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. </p> <p>10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.</p> <p>11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples. </p>
Metadata of " Stability of Selected Hydrogen Bonded Semiconductors in Organic Electronic Devices"
<p>Metadata of " Stability of Selected Hydrogen Bonded Semiconductors in Organic Electronic Devices"</p>
Benchmarking eliminative radiomic feature selection for head and neck lymph node classification - Supplemental data
<p>Supplementary files for the publication "Benchmarking eliminative radiomic feature selection for head and neck lymph node classification"</p>
Associated code and data for "Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization (doi: 10.3389/fcell.2021.74635)"
<p>This deposit contains the data, code, and analysis to reproduce the results in the manuscript - Lai X, Keller C, Santos-Rosales G, Schaft N, Dörrie J, Vera J. Multi-level computational modeling of anti-cancer dendritic cell vaccination utilized to select molecular targets for therapy optimization. Frontiers in Cell and Developmental Biolology. 2022; 9:746359; <a href="https://www.researchgate.net/publication/358461035_Multi-Level_Computational_Modeling_of_Anti-Cancer_Dendritic_Cell_Vaccination_Utilized_to_Select_Molecular_Targets_for_Therapy_Optimization">doi:10.3389/fcell.2021.746359</a>.</p> <p>If you have used the code for your research, please cite the original publication. Thank you very much.</p> <p> </p>
Raw Data of "Selective laser melting of a Fe-Si-Cr-B-C-based complex-shaped amorphous soft-magnetic electric motor rotor with record dimensions"
<p>This data set includes the RAW DATA of the publication. ABSTRACT: A record large amorphous rotor bearing an intricate 3D-geometry is produced through additive manufacturing via selecting laser melting using a powder of a traditional bulk metallic glass-forming composition of the Fe-Si-Cr-B-C system. Not only does this technique overcome the technical limitations characteristic of casting processes for amorphous alloys, but the possibility to print complex 3D geometries is expected to greatly facilitate the channeling of the magnetic flux, when such component is used as a rotor in an electric machine. The as-built part is characterized in comparison to the powder material as well as as-spun ribbons using a wide range of complementary techniques, including synchrotron x-ray diffraction, calorimetry, electron microscopy as well as room temperature ferromagnetic and hardness testing. The built part has extraordinarily high values of hardness (877 HV) and remarkable high magnetic susceptibility (9.17). This latter feature leads to a better magnetic response in the presence of an external magnetic field evidenced by a faster approach to saturation. The coercivity is small (0.51 kA/M) and the magnetic saturation relatively high (1.29 T). In addition, a large anisotropic effect on the magnetization reaction in connection with the partial crystallization in the melt pool areas is investigated experimentally.</p>
Processed Data of "Selective laser melting of a Fe-Si-Cr-B-C-based complex-shaped amorphous soft-magnetic electric motor rotor with record dimensions"
<p>This data set includes the processed data of the pubblication. ABSTRACT: A record large amorphous rotor bearing an intricate 3D-geometry is produced through additive manufacturing via selecting laser melting using a powder of a traditional bulk metallic glass-forming composition of the Fe-Si-Cr-B-C system. Not only does this technique overcome the technical limitations characteristic of casting processes for amorphous alloys, but the possibility to print complex 3D geometries is expected to greatly facilitate the channeling of the magnetic flux, when such component is used as a rotor in an electric machine. The as-built part is characterized in comparison to the powder material as well as as-spun ribbons using a wide range of complementary techniques, including synchrotron x-ray diffraction, calorimetry, electron microscopy as well as room temperature ferromagnetic and hardness testing. The built part has extraordinarily high values of hardness (877 HV) and remarkable high magnetic susceptibility (9.17). This latter feature leads to a better magnetic response in the presence of an external magnetic field evidenced by a faster approach to saturation. The coercivity is small (0.51 kA/M) and the magnetic saturation relatively high (1.29 T). In addition, a large anisotropic effect on the magnetization reaction in connection with the partial crystallization in the melt pool areas is investigated experimentally.</p>
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
<p><strong>Data associated</strong> to the study <em>Genomic signatures of isolation, hybridization, and selection during speciation of island finches</em></p> <p><strong>Contents</strong></p> <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch <em>Taeniopygia guttata</em> is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> <p>Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).</p> </li> </ul> <p> </p> <p><strong>Study summary</strong></p> <p>Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.</p>
BIOPEP-UWM: Calculations for top 23 selected peptides from ATHpin ranking of Cynara cardunculus swine blood hydrolysate FNF
<p>Calculations by BIOPEP (https://biochemia.uwm.edu.pl/biopep-uwm/) for top 23 selected peptides from ATHpin ranking of Cynara cardunculus swine blood hydrolysate FNF.</p>
Data for 'Selfish migrants: How a meiotic driver is selected to increase dispersal'
<p>Data for 'Selfish migrants: How a meiotic driver is selected to increase dispersal'</p> <p>Please refer to the README for information.</p>
Spatial patterns in neighbourhood effects on woody plant selection and bark stripping by deer in a lowland alluvial forest
<p>This dataset presents the incidence of bark stripping (present or not) and its intensity by two deer species mapped over all woody individuals ≥ 1 cm diameter at breast height (DBH). Stripping intensity was measured as the maximal percentage of the stripped stem circumference at the part of the stem with the horizontally widest stripping wound. A four-hectare square research plot is located in the Ranšpurk old-growth forest reserve in the south-eastern part of the Czech Republic (N48°40´, E16°56´).</p> <p>Several treefalls damaged the fence around the reserve in late autumn 2017, allowing fallow deer (<em>Dama dama</em> L.) and red deer (<em>Cervus elaphus</em> L.) to enter the reserve from the deer enclosure. The number of fallow deer and red deer individuals in the reserve was unknown, and likely fluctuated over time as they could enter and leave the reserve at any time. Data were collected in July 2018, ca 9–10 months after the fence was damaged. Although the fence was not fixed at the time of data collection (deer could still enter and leave the reserve), stripping wounds were not fresh and were likely received between late autumn 2017 and early spring 2018.</p> <p>The datasets includes tree and shrub individuals that fell within species-specific DBH range (susceptible individuals). The range was defined for each tree and shrub species as DBH<sub>min </sub>≤ DBH ≤ DBH<sub>max</sub>, where DBH<sub>min</sub> and DBH<sub>max</sub> are DBH of the smallest and largest stripped individuals. Individuals smaller and larger than this range were excluded from analyses, because small and large individuals may be relatively less often stripped. Woody species with ≥ 70 individuals are presented, because stochasticity does not allow meaningful spatial point pattern analyses with fewer individuals per species.</p> <p>Data contains the x and y coordinates of each individual in a local coordinate system, the woody species, its code, diameter at breast height, the incidence of stripping (present = 1 or not = 0), and the intensity of stripping (%).</p> <p> </p> <p> </p>
Selected articles from the scoping review on the study designs for clinical trials applied to personalised medicine
<p>The dataset provides the data extracted for the scoping review of the literature on the study designs for clinical trials applied to personalised medicine, as part of the EU project on “Personalised Medicine Trials” (PERMIT).</p> <p>The dataset reports the references for all articles selected as part of the scoping review, as well as information on the general study characteristics and definition, methodology, statistical considerations, and examples of each study design referred to in each included paper.</p>
Sexually antagonistic selection on educational attainment and body size in Estonian children
<p>Natural selection is a key mechanism of evolution, which results from the differential reproduction of phenotypes. We describe fecundity selection at different parity transitions on 15 anthropometric traits and educational attainment in Estonian children, who were born between 1938 and 1962 and measured at around 13 years of age (Juhan Aul’s database). The sample sizes reach up to 7000 in boys and 10 000 in girls. The direction of selection on educational attainment and bodily traits was sexually antagonistic, and it occurred via different parity transitions in boys and girls. Compared to boys with primary education, obtaining tertiary education was associated with 3.5 times and secondary education two times higher odds of becoming a father. Transition to motherhood was not related to educational attainment, while education above primary was associated with lower odds (OR = 0.5 – 0.7) to progression to parities above one and two. Selection on anthropometric traits occurred almost exclusively via childlessness in boys, while among the girls, most of the traits that were associated with becoming a mother were additionally associated with a transition from one child to higher parities. Male (but not female) fitness was thus primarily determined by traits related to mating success. Selection favoured stronger and larger boys and smaller girls. Selection on girls favoured some traits that associate with perceived femininity while other feminine traits were selected against.</p> <p>This record includes the data and R code to reproduce the statistical analyses the results are based on. </p> <p> </p>
The impact of galaxy selection on the splashback boundaries of galaxy clusters (Data)
<p>Data from O'Neil et al. (2022), The impact of galaxy selection on the splashback boundaries of galaxy clusters.</p>
Predator-based selection and the impact of edge sympatry on components of coral snake mimicry
<p>Mimicry is a vivid example of how predator-driven selection can impact phenotypic diversity, which itself can be influenced by the presence (sympatry) or absence (allopatry) of a dangerous model. However, the impact of sympatry and allopatry on predation on mimicry systems at fine spatial scales (e.g., edge sympatry, allopatry) is not well understood. We used a clay model study in a montane tropical site in Honduras to test the impact of edge sympatry on 1) overall attack rates, 2) the fitness benefit of mimetic coloration, 3) predation on specific mimetic signal components, and 4) temporal variation in predator-based selection on mimicry components. Unlike previous research, we found that mimetic phenotypes received significantly more attacks than cryptic replicas in edge sympatry, suggesting that mimetic phenotypes might not confer a fitness benefit in areas of edge sympatry. Additionally, we documented temporal variation in predator-based selection, as the impacts of allopatry on predatory attacks varied among years. Our results imply that the effect of sympatry and allopatry on predator-based selection in mimicry systems may be more complex than previously thought for species-rich assemblies of coral snakes and their mimics in the montane tropics.</p>
Data for: Sexual dichromatism may not be a good index of sexual or natural selection in the blue cardinalids (Aves: Passeriformes).
<p>More than a century ago, Darwin and Wallace started a still ongoing debate over which are the predominant forces driving sexual dichromatism (i.e., differences in body coloration between males and females): is it sexual selection on males to become more attractive, or is it natural selection on females to become more cryptic? While these are not mutually exclusive, the degree of sexual dichromatism has been extensively used as a proxy of the intensity of one type of selection (sexual) on one of the sexes (males). Here, we evaluated the relationship between sexual dichromatism and two body-color features that can be under natural and/or sexual selection in each sex: conspicuousness against the background and colorfulness (which we defined as the variety of colors and mechanisms to produce them within an individual's plumage). We focused on the 'blue clade' of the Cardinalidae bird family and considered the properties of their own visual system and those of potential raptor predators. We found that all blue cardinalids are sexually dichromatic, but levels of dichromatism vary within the clade. Males are on average more colorful than females, but neither male nor female colorfulness correlates with sexual dichromatism. Males are not more conspicuous than females against a vegetated background but are significantly more conspicuous against a nesting background than females. Yet, we found no correlation between conspicuousness and degree of sexual dichromatism. Our results suggest that, while both natural and sexual selection can drive color differences between the sexes, levels of sexual dichromatism do not necessarily reflect intensity of selection forces in this clade. Our results highlight the importance of testing assumptions regarding the relationship between sexual dichromatism and color evolution in each sex, considering the properties of different visual systems, relevant to the ecology of the study model.</p>
Tool for the selection of indicators for agriculture sustainability assessment
<p>This is a preliminary version of the Excel-based tool that is being developed within the Working Group of the Crop diversification cluster on Multi-criteria Assessment and Sustainability Indicators (MCA & SI cluster WG). The tool has the aim to assist different end-users in the selection of sustainability indicators tailored to assess the impacts and effects of crop diversification. Currently this preliminary version contains only the indicators developed by the DiverIMPACTS and DiverFARMING projects (2 out 5 projects of Crop diversification cluster).</p> <p>The tool is composed by three sheets: 1) the “Selection” sheet for querying the database and obtaining the results; 2) the “Database” sheet where all indicators of the cluster projects are reported; 3) the “SAFA_HierachicalClassification” sheet with the description of the SAFA framework, and the items identified for the indicators of the cluster projects reported in the database.</p>
GEOS CCM free-running simulation data of the Pacific-Northwest pyrocumulonimbus Event-like aerosol injection, SWIRL selection
<p>Data from GEOS CCM free running simulation of the Pacific-Northwest pyrocumulonimbus Event. </p> <p>The simulations have been designed and performed by Sampa Das and Peter R. Colarco at the NASA Center for Climate Simulations; the computing resources supporting the simulations shown in this work were provided by the NASA High-End Computing (HEC) Program through the NASA Center for Climate Simulation (NCCS) at the Goddard Space Flight Center.</p> <p>The datasets stored here have been generated by Giorgio Doglioni starting from the whole results of the simulations.</p> <p>The files are in hdf5 format and their structure and content is described in the README file. </p> <p> </p>
Fig. 2 in Associations Between Habitat Quality And Body Size In The Carpathian-Podolian Land Snail Vestia Turgida: Species Distribution Model Selection And Assessment Of Performance
Fig. 2. Linear relationship (solid line) and 95 % confidence interval (gray area) between habitat quality predicted by the BART model (x-axis) and shell height (H in millimeters, y-axis), derived from the linear mixed model.
Fig. 4. Partial dependence plot for topographic Fig. 5 in Associations Between Habitat Quality And Body Size In The Carpathian-Podolian Land Snail Vestia Turgida: Species Distribution Model Selection And Assessment Of Performance
Fig. 4. Partial dependence plot for topographic Fig. 5. Partial dependence plot for terrain roughness wetness index (TWI). index (tri).
Fig. 6 in Associations Between Habitat Quality And Body Size In The Carpathian-Podolian Land Snail Vestia Turgida: Species Distribution Model Selection And Assessment Of Performance
Fig. 6. Partial dependence plot for pH water (phh2o). Fig. 7. Partial dependence plot for silt content (SLT).
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.