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.
28
datasets available to search
ShareScore release 0.9.0
Dataset results
28 results for “Restricted selection”
Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters
<p>The input and main output files used for the paper <em><strong>"Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters"</strong></em> are separated in the different tar files depending the MD stage they belong to.</p> <p><strong>Content</strong></p> <p>00_AlphaFold2: The models predicted from AlphaFold2</p> <p>01_build_system: The parameters for ATP and the initial pdb file used to build each system</p> <p>02_minimization: Minimization input files for each variant</p> <p>03_equilibration: Equilibration input files for each variant</p> <p>04_long_equilibration: ATP restrained equilibration input files for each variant</p> <p>05_free_equilibration: Free equilibration input files for each variant</p> <p>06_production: Free production input files for each variant</p> <p>07_caver: Caver calculations for each variant and replica</p> <p>08_transport_tools: Analysis of tunnel networks using TransportTools software</p> <p>09_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments</p> <p>10_caverdock: CaverDock calculations for each variant and for each ligand tested</p> <p>11_membrane_patch: MD simulations for liquiritigenin and POPC membrane only</p> <p>12_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11 (not for APO). Calculation of X1 and X2 angles for residue N1331 in each variant (not for APO)</p> <p>13_US_closed_to_open: Umbrella Sampling simulations to obtain the inward facing (IF) open state of each variant. Not used for PMF analysis.</p> <p>14_US_opening_energy: Umbrella Sampling simulations to obtain the Potential of Mean Force for the transition from IF-closed to IF-open conformations.</p> <p>15_US_equilibration: Equilibration input files for WT and F562L variants in IF-open states.</p> <p>16_US_production: Production input files for WT and F562L variants in IF-open states.</p> <p>17_US_caver: Caver calculations for WT and F562L variants in IF-open states.</p> <p>18_US_transport_tools: Analysis of tunnel networks using TransportTools software of WT and F562L variants in IF-open states.</p> <p>19_US_tunnel_selection: Selection of the tunnels with widest bottleneck radius to perform CaverDock experiments for WT and F562L variants in IF-open states.</p> <p>20_US_caverdock: CaverDock calculations for WT and F562L variants in IF-open states.</p> <p>21_US_MD_analysis: Calculations of RMSD, RMSF of each system. Calculation of helical parameters for trans-membrane helices 2, 5, 8 and 11.</p> <p>ABC_Sequences.fasta: Sequences from 1KP analysis</p>
Figure 1 in Testing the habitat selectivity of bdelloid rotifers in a restricted area
Figure 1. Geographic localisation of the 90 samples in the six habitats. Coordinates are expressed as latitude and longitude in decimal degrees.
Restricted language access during childhood affects adult brain structure in selective language regions
<p>Anatomical measurements data and analysis codes in R used in manuscript 'Restricted language access during childhood affects adult brain structure in selective language regions'.</p>
Lack of pollinators selects for increased selfing, restricted gene flow and resource allocation in the rare Mediterranean sage Salvia brachyodon
<p>Salvia brachyodon (Lamiaceae): raw data on flower morphometry, nectar concentration and volume and seed weight according various pollination treatments.</p>
Accompanying data set for the manuscript "REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention"
<p>This data set contains all experimental and theoretical data included in the manuscript " REverSe TRanscrIptase Chain Termination (RESTRICT) for Selective Measurement of Nucleotide Analogs Used in HIV Care and Prevention", namely:</p> <p>RESTRICT_model: MATLAB script for completing calculations in the RESTRICT theoretical model.</p> <p>Figure 2:</p> <ul> <li>Raw data from theoretical model showing contributions of individual model components, Kaff = 0.3</li> <li>Normalized data from theoretical model showing contributions of individual model components, Kaff = 0.3</li> <li>Experimental NRTI Drug Screen 180 nt TTCA 500 nM dNTP</li> </ul> <p>Figure 3:</p> <ul> <li>Experiment-dNTP-Concentration-Screen</li> <li>Theory-dNTP-Concentration-Screen</li> <li>Experiment-Template-Length-Screen</li> <li>Theory-Template-Length-Screen</li> <li>Experiment-Sequence-Screen</li> <li>Theory-Sequence-Screen</li> </ul> <p>Figure 4:</p> <ul> <li>Experimental-NRTI-Drug-Screen-90nt-TCAA-only</li> <li>Theory-TCAA90-Kaff=0point2</li> <li>Experimental-NRTI-Drug-Screen-GGCA-only</li> <li>Theory-GGCA180-Kaff=0point2</li> </ul> <p>Figure 5:</p> <ul> <li>GGCA-vs-TTCA-Specificity-Analysis</li> </ul>
Data from: Effective implementation of age restrictions increases selectivity of sport hunting of the African lion
1. Sport hunting of wildlife can play a role in conservation but can also drive population declines if not managed sustainably. Previous simulation modelling found that large felid species could theoretically be hunted sustainably by restricting harvests to older individuals that have likely reproduced. Several African countries currently use age-based hunting for lions although the outcomes have yet to be evaluated in a wild population. 2. Here we provide the first empirical evidence that a system of incentives sufficiently encouraged age-based hunting and reduced offtake of a wild felid, thereby reducing the potential risk of unsustainable hunting on a threatened species. We examined long-term hunting data and the lion population trend in Niassa National Reserve, Mozambique. 3. To incentivise hunter compliance, a 'points' system was developed which rewards operators that harvest lions older than the 6-year minimum trophy age recommended for sustainable hunting and penalises operators that hunt 'underage' lions (<4 years). A key component of this system is the ecological application of key physical traits that predictably change with age in order to estimate (by hunters) and validate (by authorities) trophy individuals' ages pre- and post-mortem, respectively. Analysis of 138 lion hunts and 87 lion trophies from 2003-2015 revealed that after enforcement of age restrictions in 2006, hunters shifted harvests to suitably aged lions (>6 years), from 25% of offtakes in 2004 to 100% by 2014. 4. Simultaneously, the number of lions and percentage of quota harvested decreased, resulting in lower lion offtakes. Following an initial decrease after enforcement of the aging system, the percentage of hunts harvesting lions stabilised, demonstrating that hunters successfully located and aged older lions. 5. Synthesis and applications. Evidence suggests that age restrictions combined with an incentive-based points system regulated sport hunting and reduced pressure on the lion population. We attribute the successful implementation of this management system to: 1) committed, consistent enforcement by management authorities, 2) genuine involvement of all stakeholders from the start, 3) annual auditing by an independent third party, 4) the reliable, transparent, straight-forward aging process, and 5) the simple, pragmatic points system for incentivising hunter compliance. Our study demonstrates that the use of age restrictions can increase the selectivity of sport hunting and lower trophy offtakes to reduce the possibility of unsustainable sport hunting negatively impacting species populations in the absence of reliable estimates of population size. It must be noted, however, that there was no measurable change in the lion numbers over the past decade that could be attributed to the implementation of this policy alone.
Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection
While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained by (i) the native source populations from which they were derived and (ii) demographic bottlenecks during introduction. Genetic data indicated a localized source area for most sampled invasive populations, with limited evidence for admixing of native source populations. This pattern largely coincides with historical data on pet trade exports. However, the invasive populations are genetically more similar than predicted from the export data alone. The extent of bottleneck effects varied among invasive populations. The observed low genetic diversity, evidence of demographic contraction and restricted source area do not support the hypothesis that invasion is favoured by the mixing and recombining of genetic variation from multiple source populations. Instead, they suggest that reduced genetic variation through random processes may not inhibit successful establishment and invasion in this species. However, convergent selection across invasive sites could also explain the observed patterns of reduction and similarity in genetic variation and/or the restricted source area. In general, the alternative explanation of intraspecific variation in invasive potential among genotypes or geographic areas is neglected, but warrants more attention as it could inform comparative studies and management of biological invaders.
Data from: Ecological segregation in a small mammal hybrid zone: habitat-specific mating opportunities and selection against hybrids restrict gene flow on a fine spatial scale
The degree to which closely related species interbreed is determined by a complex interaction of ecological, behavioral, and genetic factors. We examine the degree of interbreeding between two woodrat species, Neotoma bryanti and N. lepida, at a sharp ecological transition. We identify the ecological association of each genotypic class, assess the opportunity for mating between these groups, and test whether they have similar patterns of year-to-year persistence on our study site. We find that 13% of individuals have a hybrid signature but that the two parental populations and backcrosses are highly segregated by habitat type and use. Also, we find that adult hybrids are comparable to parental types in terms of year-to-year persistence on our site but that, among juveniles, significantly fewer hybrids reach adulthood on site compared to their purebred counterparts. Our analyses show that this hybrid zone is maintained by occasional nonassortative mating coupled with hybrid fertility, but that these factors are balanced by lower apparent survival of juvenile hybrids and habitat-based preference or selection that limits heterospecific mating while promoting backcrossing to habitat-specific genotypes. This system presents a novel example of the role that sharp resource gradients play in reproductive isolation and the potential for genetic introgression.
Selective Fetal Growth Restriction in Monochorionic Twins - an International Investigation
ClinicalTrials.gov study NCT05952583. IPD Sharing: UNDECIDED. Countries: 6. Publications: 0.
Data from: Effective implementation of age restrictions increases selectivity of sport hunting of the African lion
Open the record for dataset details and reuse information.
Data from: Shared genetic diversity across the global invasive range of the Monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection
Open the record for dataset details and reuse information.
Data from: Ecological segregation in a small mammal hybrid zone: habitat-specific mating opportunities and selection against hybrids restrict gene flow on a fine spatial scale
Open the record for dataset details and reuse information.
Data from: The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing
Next-generation sequencing (NGS) techniques are now key tools in the detection of population genomic and gene expression differences in a large array of organisms. However, so far few studies have utilized such data for phylogenetic estimations. Here, we use NGS data obtained from genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to estimate the phylogenetic relationships among all 26 species of swordtail and platyfish (genus Xiphophorus) from Central America. Past studies, both sequence and morphology-based, have differed in their inferences of the evolutionary relationships within this genus, particularly at the species-level and among monophyletic groupings. We show that using a large number of markers throughout the genome, we are able to infer the phylogenetic relationships with unparalleled resolution for this genus. The relationships among all three major clades and species within each of them are highly resolved and consistent under maximum likelihood, Bayesian inference and maximum parsimony. However, we also highlight the current cautions with this data type and analyses. This genus exhibits a particularly interesting evolutionary history where at least two species may have arisen through hybridization events. Here, we are able to infer the paternal lineages of these putative hybrid species. Using the RAD-marker-based tree we reconstruct the evolutionary history of the sexually selected sword trait and show that it may have been present in the common ancestor of the genus. Together our results highlight the outstanding capacity that RAD sequencing data has for resolving previously problematic phylogenetic relationships, particularly among relatively closely related species.
Data from: The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing
Open the record for dataset details and reuse information.
The m6A reader Ythdf restricts axonal growth in Drosophila through target selection modulation of the Fragile X mental retardation protein
GEO Series GSE145342. Drosophila melanogaster. 6 samples. Type: Expression profiling by high throughput sequencing.
Single-cell insights into trophoblast heterogeneity and adaptive dysfunction in selective fetal growth restriction
GEO Series GSE314816. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
A double negative thymocyte specific enhancer augments Notch1 signaling to direct early T cell progenitor expansion, lineage restriction and b-selection.
GEO Series GSE211079. Mus musculus. 34 samples. Type: Expression profiling by high throughput sequencing.
The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4/UL5 Transcripts
GEO Series GSE159853. Homo sapiens. 54 samples. Type: Expression profiling by high throughput sequencing; Other.
Development of miRNA expression signatures for selective intrauterine growth restriction (sIUGR) in two fetus placenta tissues
GEO Series GSE98146. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by array.
Ythdf modulates Fmr1 target selection and restricts axonal growth in Drosophila
GEO Series GSE161655. Drosophila melanogaster. 27 samples. Type: Expression profiling by high throughput sequencing.
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.