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.
2,315
datasets available to search
ShareScore release 0.7.1
Dataset results
2,315 results for “maintainability”
Dataset accompanying Riesch et al. 2020. Grazing by wild red deer maintains characteristic vegetation of semi-natural open habitats: Evidence from a 3-year exclusion experiment. Applied Vegetation Science
<p>This repository contains vegetation community data used by Riesch et al. 2020 in an article accepted in Applied Vegetation Science.</p> <p>Metadata are provided in the first excel worksheet. For further details please see the original article.</p>
Tissue-resident memory Th17 cells maintain stable fungal commensalism in the oral mucosa
<p>Raw data files linked to a manuscript published in Mucosal Immunology 2020 (accepted for publication on July 6th,.2020)</p>
Data from: Cost of an elaborate trait: a tradeoff between attracting females and maintaining a clean ornament
<p><span><span><span><span><span><span><span><span><span><span><span>Many sexually selected ornaments and weapons are elaborations of an animal's outer body surface, including long feathers, colorful skin, and rigid outgrowths. The time and energy required to keep these traits clean, attractive, and in good condition for signaling may represent an important, but understudied cost of bearing a sexually selected trait. Male fiddler crabs possess an enlarged and brightly colored claw that is used both as a weapon to fight with rival males and also as an ornament to court females. Here, we demonstrate that males benefit from grooming because females prefer males with clean claws over dirty claws, but also that the time spent grooming detracts from the amount of time available for courting females. Males therefore face a temporal tradeoff between attracting the attention of females and maintaining a clean claw. Our study provides rare evidence of the importance of grooming for mediating sexual interactions in an invertebrate, indicating that sexual selection has likely shaped the evolution of self-maintenance behaviors across a broad range of taxa.</span></span></span></span></span></span></span></span></span></span></span></p>
During hippocampal inactivation, grid cells maintain synchrony, even when the grid pattern is lost
<p>The grid cell network in the medial entorhinal cortex (MEC) has been subject to thorough testing and analysis, and many theories for their formation have been suggested. To test some of these theories, we re-analyzed data from Bonnevie et al., 2013, in which the hippocampus was inactivated and grid cells were recorded in the rat MEC. We investigated whether the firing associations of grid cells depend on hippocampal inputs. Specifically, we examined temporal and spatial correlations in the firing times of simultaneously recorded grid cells before and during hippocampal inactivation. Our analysis revealed evidence of network coherence in grid cells even in the absence of hippocampal input to the MEC, both in regular grid cells and in those that became head-direction cells after hippocampal inactivation. This favors models, which suggest that phase relations between grid cells in the MEC are dependent on intrinsic connectivity within the MEC.</p>
Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations
<p>Standard infectious disease practice calls for aggressive drug treatment that rapidly eliminates the pathogen population before resistance can emerge. When resistance is absent, this elimination strategy can lead to complete cure. However, when resistance is already present, removing drug-sensitive cells as quickly as possible removes competitive barriers that may slow the growth of resistant cells. In contrast to the elimination strategy, the containment strategy aims to maintain the maximum tolerable number of pathogens, exploiting competitive suppression to achieve chronic control. Here we combine <em>in vitro</em> experiments in computer-controlled bioreactors with mathematical modeling to investigate whether containment strategies can delay failure of antibiotic treatment regimens. To do so, we measured the "escape time" required for drug-resistant <em>E. coli</em> populations to eclipse a threshold density maintained by adaptive antibiotic dosing. Populations containing only resistant cells rapidly escape the threshold density, but we found that matched resistant populations that also contain the maximum possible number of sensitive cells could be contained for significantly longer. The increase in escape time occurs only when the threshold density--the acceptable bacterial burden--is sufficiently high, an effect that mathematical models attribute to increased competition. The findings provide decisive experimental confirmation that maintaining the maximum number of sensitive cells can be used to contain resistance when the size of the population is sufficiently large.</p>
Male fairy-wrens produce and maintain vibrant breeding colours irrespective of individual quality
<p>Conspicuous colours may signal individual quality if high-quality individuals produce more elaborate colours or have a greater capacity to invest in colour maintenance. We investigate these hypotheses using repeated within-individual observations and experimentally-induced colour production in a wild bird, the superb fairy-wren (Malurus cyaneus). Male superb fairy-wrens undergo an annual moult from brown, non-breeding plumage to an ultraviolet-blue and black breeding plumage. Colour maintenance is especially relevant for this species because structural, ultraviolet-blue plumage colours are particularly susceptible to fading. Further, only the most sexually attractive males moult to breeding plumage early (before spring) and thereby keep their colours for an extended time before the breeding season. Our results show that (i) sexually attractive, early-moulting males do not have higher quality breeding colours and (ii) breeding colours are not impacted by experimentally inducing males to moult early and while in low body condition. We found that (iii) breeding colours do not fade but remain consistent or become more saturated within individuals over time. Despite this, (iv) males do not spend more time preening while in breeding plumage. Instead, males keep their colours in pristine condition by re-moulting parts of their breeding plumage throughout the breeding season, suggesting an alternative, potential cost of maintaining ornamental colours. We conclude that variation in structural breeding colours is unlikely to indicate individual quality in superb fairy-wrens.</p>
Software maintainability prediction
<p>The pre-processing techniques were applied in the bug prediction datasets published in http://bug.inf.usi.ch/download.php by <a href="http://www.inf.unisi.ch/phd/dambros/">D'Ambros</a> et al to produce a new version of these datasets that are suitable for software maintainability prediction. The independent variables are CK and OO metrics and the dependent variables is CHANGE metric.</p>
Data for: Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size
<p>Coevolutionary negative frequency-dependent selection has been hypothesized to maintain genetic variation in host and parasites. <br> Despite the extensive literature pertaining to host-parasite coevolution, the dynamics of genetic variation has not been examined in a matching-alleles model (MAM) with a finite population size relative to the expectation under neutral genetic drift alone. The dynamics of the MA coevolution in an infinite population, in fact, suggests that genetic variation in these coevolving populations behaves neutrally. By comparing host heterozygosity to the expectation in a single-species model of neutral genetic drift we find that while this is also largely true in finite populations two additional phenomena arise. First, reciprocal natural selection acting on stochastic perturbations in host and pathogen allele frequencies results in a slight increase or decrease in genetic variation depending on the parameter conditions. Second, following the fixation of an allele in the parasite, selection in the MAM becomes directional, which then rapidly erodes genetic variation in the host. Hence, rather than maintain it, we find that, on average, matching-alleles coevolution depletes genetic variation.</p>
Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats
Supplementation of wild populations with captive-bred individuals is often ineffective for boosting long-term productivity of wild populations. On the other hand, it remains unknown whether supplementation can act to maintain life-history variation in natural habitats, which is also important for the long-term persistence of populations and species. Partial migration, in which both migratory and resident individuals are maintained in a population, is commonly found across animal taxa. However, human-induced habitat fragmentation continues to cause rapid decline in a migratory phenotype among many natural populations. By using field and hatchery experiments, we here demonstrated that while migrants and residents could be maintained in captive environments, few fish became migrants in natural streams in red-spotted masu salmon Oncorhynchus masou ishikawae. Released captive-bred fish rarely reached the threshold body size necessary to become migrants in natural streams, presumably due to lower growth condition in natural than in captive environments. The decision to migrate is often considered a threshold trait in salmonids and other animal taxa. Our findings highlight the need for supplementation programs to acknowledge environmentally induced changes in life-history decisions for partially migratory species.
Data from: Sexual selection maintains a female-specific character in a species with dynamic sex roles
The effects of sexual selection are more conspicuous among male animals, and as a result the majority of sexual selection research focuses on males. However, burgeoning evidence suggests that sexual selection also acts on females, and there have been calls for an increased focus on females. Here, we used a multivariate approach to analyze sexual selection in Kawanaphila nartee, a spermatophore gift-giving bushcricket with dynamic sex roles. Early in the breeding season females compete for males, and later, when environmental food resources are more abundant, sex roles revert to Darwinian convention. Ear size, which is much greater in females than in males, has been suggested to affect female fitness, as females with larger ears are more likely to reach calling males first under sex role reversed conditions. We tested this suggestion and found evidence of positive linear and nonlinear correlational selection acting on female ear size early in the breeding season (under reversed sex roles), but not later in the breeding season (under Darwinian sex roles). Interestingly, there was no correlation between mating success and reproductive success (Bateman gradient) at any time during the season. Together, our results indicate that even brief and circumscribed periods of intrasexual competition among females can lead to sexual selection on morphological characters, and that this selection may not depend on multiple mating. Considering the wealth of reports in the literature of brief episodes of intrasexual competition among female animals, we recommend increased study of sexual selection acting on females.
Herding mechanisms to maintain the cohesion of a harem group: two interaction phases during herding
<p>In animal groups, individual interactions achieve coordinated movements to maintain cohesion. In horse harem groups, herding<br> is a behavior in which males chase females from behind; it is considered to assist with group cohesiveness. However,<br> the mechanisms by which the individuals move to maintain group cohesion are unknown. We applied novel non-invasive<br> methods of drone filming and video tracking to observe horse movements in the field with high temporal and spatial resolution.<br> We tracked all group members and drew trajectories. We analyzed the movements of females and found two phases<br> of interactions based on their timing of movement initiation. The females that moved first were those nearest to the herding<br> male, while the movement initiation of the later females was determined by the distance from the nearest moving female, not<br> by the distance from the herding male. These interactions are unique among animal group movements and might represent a<br> herding mechanism responsible for maintaining group cohesion. This might be due to long-term stable relationships within<br> a harem group and strong social bonds between females. This study showed that the combination of drone filming and video<br> tracking is a useful method for analyzing the movements of animals simultaneously in high resolution.</p>
Data from: Flightin maintains myofilament lattice organization required for optimal flight power and courtship song quality in Drosophila
The indirect flight muscles (IFMs) of Drosophila and other insects with asynchronous flight muscles are characterized by a crystalline myofilament lattice structure. The high-order lattice regularity is considered an adaptation for enhanced power output, but supporting evidence for this claim is lacking. We show that IFMs from transgenic flies expressing flightin with a deletion of its poorly conserved N-terminal domain (flnΔN62) have reduced inter-thick filament spacing and a less regular lattice. This resulted in a decrease in flight ability by 33% and in skinned fibre oscillatory power output by 57%, but had no effect on wingbeat frequency or frequency of maximum power output, suggesting that the underlying actomyosin kinetics is not affected and that the flight impairment arises from deficits in force transmission. Moreover, we show that flnΔN62 males produced an abnormal courtship song characterized by a higher sine song frequency and a pulse song with longer pulses and longer inter-pulse intervals (IPIs), the latter implicated in male reproductive success. When presented with a choice, wild-type females chose control males over mutant males in 92% of the competition events. These results demonstrate that flightin N-terminal domain is required for optimal myofilament lattice regularity and IFM activity, enabling powered flight and courtship song production. As the courtship song is subject to female choice, we propose that the low amino acid sequence conservation of the N-terminal domain reflects its role in fine-tuning species-specific courtship songs.
Spatial and temporal heterogeneity in pollinator communities maintains within-species floral odour variation
<p>Flowering plants emit complex bouquets of volatile organic compounds (VOCs) to mediate interactions with their pollinators. These bouquets are undoubtedly influenced by pollinator-mediated selection, particularly in deceptively-pollinated species that rely on chemical mimicry. However, many uncertainties remain regarding how spatially and temporally heterogeneous pollinators affect the diversity and distribution of floral odour variation. Here, we characterized and compared the floral odours of ten populations of deceptively-pollinated <em>Arum maculatum</em> (Araceae), and inter-annual and decadal variation in pollinator attraction within these populations. Additionally, we transplanted individuals from all sampled populations to two common garden sites dominated by different pollinator species (<em>Psychoda phalaenoides</em> or <em>Psycha grisescens</em>), and compared pollinator attraction rates to investigate whether populations maintained odour blends adapted to a specific pollinator. We identified high within- and among-population variation in a common blend of VOCs found across the range of <em>A. maculatum</em>. We also observed shifts in pollinator community composition within several populations over 1-2 years, as well as over the past decade. Common garden experiments further revealed that transplanted inflorescences generally attracted the dominant local pollinator species in both transplant sites. However, one population (Forêt du Gâvre, France) appears to exclusively attract <em>P. grisescens</em>, even when transplanted to a <em>P. phalaenoides</em>-dominated site. Together, our results suggest that maintaining diverse floral odour bouquets within populations may be advantageous when pollinator communities vary over short timescales. We propose that temporally-replicated ecological data are one potential key to understanding variation in complex traits such as floral odour, and in some cases may reveal resiliency to shifting pollinator communities.</p>
The potential for genotype-by-environment interactions to maintain genetic variation in a model legume–rhizobia mutualism
<p>The maintenance of genetic variation in mutualism-related traits is key for understanding mutualism evolution, yet the mechanisms maintaining variation remain unclear. We asked whether genotype-by-environment (G×E) interaction is a potential mechanism maintaining variation in the model legume–rhizobia system, <em>Medicago truncatula–Ensifer meliloti</em>. We planted 50 legume genotypes in a greenhouse under ambient light and shade to reflect reduced carbon availability for plants. We found an expected reduction under shaded conditions for plant performance traits, such as leaf number, aboveground and belowground biomass, and a mutualism-related trait, nodule number. We also found G×E for nodule number, with ∼83% of this interaction due to shifts in genotype fitness rank order across light environments, coupled with strong positive directional selection on nodule number regardless of light environment. Our results suggest that G×E can maintain genetic variation in a mutualism-related trait that is under consistent positive directional selection across light environments.</p>
Data from: Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.
Learning‐induced switching costs in a parasitoid can maintain diversity of host aphid phenotypes although biocontrol is destabilized under abiotic stress
<p>Aphid populations frequently include phenotypes that are resistant to parasitism by hymenopterous parasitoid wasps, which is often attributed to the presence of 'protective' facultative endosymbionts residing in aphid tissues, particularly <em>Hamiltonella defensa</em>. In field conditions, under parasitoid pressure, the observed coexistence of aphids with and without protective symbionts cannot be explained by their difference in fitness alone.</p> <p>Using the cereal aphid <em>Rhopalosiphum padi</em> as a model, we propose an alternative mechanism whereby parasitoids are more efficient at finding common phenotypes of aphid and experience a fitness cost when switching to the less common phenotype.</p> <p>We construct a model based on delay differential equations and parameterise and validate the model with values within the ranges obtained from experimental studies. We then use it to explore possible effects on system dynamics under conditions of environmental stress, using our existing data on the effects of drought stress in crops as an example.</p> <p>We show the 'switching penalty' incurred by parasitoids leads to stable coexistence of aphids with and without <em>H. defensa</em> and provides a potential mechanism for maintaining phenotypic diversity amongst host organisms. We show that drought-induced reduction in aphid development time has little impact. However, greater reduction in fecundity on droughted plants of symbiont-protected aphids can cause insect population cycles when the system would be stable in the absence of drought stress.</p> <p>The stabilising effect of the increased efficiency in dealing with more commonly encountered host phenotypes is applicable to a broad range of consumer-resource systems and could explain stable coexistence in competitive environments. The loss of stable coexistence when drought has different effects on the competing aphid phenotypes highlights the importance of scenario testing when considering biocontrol for pest management.</p>
Data from: Evidence for hybridisation-driven heteroplasmy maintained across generations in a ricefish endemic to a Wallacean ancient lake
<p><span>Heteroplasmy, </span><span>the presence of multiple mitochondrial DNA (mtDNA) haplotypes within cells of an individual,</span><span> is caused by mutation or paternal leakage. However, heteroplasmy is usually resolved to homoplasmy within a few generations because of germ-line bottlenecks; therefore, instances of heteroplasmy are limited in nature. Here, we report </span><span>heteroplasmy in the ricefish species <em>Oryzias matanensis</em>, endemic to Lake Matano, an ancient lake in Sulawesi Island, in which one individual was known to have many heterozygous sites in the <span class="shorttext">mitochondrial NADH dehydrogenase subunit 2 (ND2) gene</span>. </span><span>In this study, </span><span>we cloned the ND2 gene for some additional individuals with heterozygous sites and demonstrated that they are truly heteroplasmic. Phylogenetic analysis revealed that the extra haplotype within the heteroplasmic <em>O. matanensis</em> individuals clustered with haplotypes of </span><em><span>O. marmoratus</span></em><span>, a congeneric species inhabiting adjacent lakes. This indicated that the heteroplasmy originated from paternal leakage due to interspecific hybridisation. </span><span>The extra haplotype was unique and contained </span><span>t</span><span>wo</span><span> nonsynonymous substitutions. </span><span>These findings demonstrate that this hybridisation-driven heteroplasmy was maintained across generations for a long time to the extent that the extra mitochondria evolved within the new host.</span></p>
Commensal bacteria maintain a Qa-1b-restricted unconventional CD8+ T population in gut epithelium
<p>Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+ T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+ T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigens, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Interestingly, monocolonization with <em>Pediococcus pentosaceus</em>, which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.</p>
A distinct isoform of lymphoid enhancer binding factor 1 (LEF1) epigenetically restricts EBV reactivation to maintain viral latency
<p>As a human tumor virus, EBV is present as a latent infection in its associated malignancies where genetic and epigenetic changes have been shown to impede cellular differentiation and viral reactivation. We reported previously that levels of the Wnt signaling effector, lymphoid enhancer binding factor 1 (LEF1) increased following EBV epithelial infection and an epigenetic reprogramming event was maintained even after loss of the viral genome. Elevated LEF1 levels are also observed in nasopharyngeal carcinoma and Burkitt lymphoma. To determine the role played by LEF1 in the EBV life cycle, we used in silico analysis of EBV type 1 and 2 genomes to identify over 20 Wnt-response elements, which suggests that LEF1 may bind directly to the EBV genome and regulate the viral life cycle. Using CUT&RUN-seq, LEF1 was shown to bind the latent EBV genome at various sites encoding viral lytic products that included the immediate early transactivator BZLF1 and viral primase BSLF1 genes. The LEF1 gene encodes various long and short protein isoforms. siRNA depletion of specific LEF1 isoforms revealed that the alternative-promoter derived isoform with an N-terminal truncation (∆N LEF1) transcriptionally repressed lytic genes associated with LEF1 binding. In addition, forced expression of the ∆N LEF1 isoform antagonized EBV reactivation. As LEF1 repression requires histone deacetylase activity through either recruitment of or direct intrinsic histone deacetylase activity, siRNA depletion of LEF1 resulted in increased histone 3 lysine 9 and lysine 27 acetylation at LEF1 binding sites and across the EBV genome. Taken together, these results indicate a novel role for LEF1 in maintaining EBV latency and restriction viral reactivation via repressive chromatin remodeling of critical lytic cycle factors.</p>
Mesophotic corals in Hawaii maintain autotrophy to survive low-light conditions: Stable isotope dataset
<p>In mesophotic coral ecosystems, reef-building corals and their photosynthetic symbionts can survive with less than 1% of surface irradiance. How depth-specialist corals rely upon autotrophically and heterotrophically-derived energy sources across the mesophotic zone remains unclear. We analyzed the stable carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) isotope values of a <em>Leptoseris </em>community from the ʻAuʻau Channel, Maui, Hawaiʻi (65-125 m) including four coral host species living symbiotically with three algal haplotypes. We characterized the isotope values of hosts and symbionts across species and depth to compare trophic strategies. Symbiont δ<sup>13</sup>C was consistently 0.5‰ higher than host δ<sup>13</sup>C at all depths. Mean colony host and symbiont δ<sup>15</sup>N differed by up to 3.7‰ at shallow depths and converged at deeper depths. These results suggest that both heterotrophy and autotrophy remained integral to colony survival across depth. The increasing similarity between host and symbiont δ<sup>15</sup>N at deeper depths suggests that nitrogen is more efficiently shared between mesophotic coral hosts and their algal symbionts to sustain autotrophy. Isotopic trends across depth did not generally vary by host species or algal haplotype, suggesting that photosynthesis remains essential to <em>Leptoseris </em>survival and growth despite low light availability in the mesophotic zone.</p>
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.