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.
13,864
datasets available to search
ShareScore release 0.9.0
Dataset results
13,864 results for “staging”
MAP 10 in Biology, immature stages, and systematics of snail-killing flies of the genus Colobaea (Diptera: Sciomyzidae), with overviews of aspects of the tribe Sciomyzini
MAP 10. Geographic range of Colobaea limbata (Hendel).
MAP 15 in Biology, immature stages, and systematics of snail-killing flies of the genus Colobaea (Diptera: Sciomyzidae), with overviews of aspects of the tribe Sciomyzini
MAP 15. Geographic range of Colobaea punctata (Lundbeck).
Data from: Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon
Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the environment, including water salinity, exposure to pathogens, and shift in dietary lipid availability. Many anticipatory changes in physiology occur before migration to sea, but little is known about the molecular nature of these changes. Here we use a long term feeding experiment to study transcriptional regulation of lipid metabolism in Atlantic salmon gut and liver in both fresh- and saltwater. We find that lipid metabolism is highly plastic in response to differences in dietary lipid composition in freshwater, but then undergoes a marked shift when salmon transitions to the marine life-stage. Expression of genes in liver relating to lipogenesis and lipid transport decrease overall and become less responsive to diet, while genes for lipid uptake in gut become more highly expressed. Finally, analyses of evolutionary consequences of the salmonid specific whole-genome duplication on lipid metabolism reveals several pathways with significantly different (p<0.05) duplicate retention or duplicate regulatory conservation. We also find a limited number of cases where the whole genome duplication has resulted in an increased gene dosage. Our results demonstrate the presence of a life-stage associated remodeling of lipid metabolism at the gene regulatory level, suggesting an evolved preparatory optimization of lipid metabolism
Data from: Perceived duration of brief visual events is mediated by timing mechanisms at the global stages of visual processing
There is a growing body of evidence pointing to the existence of modality-specific timing mechanisms for encoding sub-second durations. For example, the duration compression effect describes how prior adaptation to a dynamic visual stimulus results in participants underestimating the duration of a sub-second test stimulus when it is presented at the adapted location. There is substantial evidence for the existence of both cortical and pre-cortical visual timing mechanisms; however, little is known about where in the processing hierarchy the cortical mechanisms are likely to be located. We carried out a series of experiments to determine whether or not timing mechanisms are to be found at the global processing level. We had participants adapt to random dot patterns that varied in their motion coherence, thus allowing us to probe the visual system at the level of motion integration. Our first experiment revealed a positive linear relationship between the motion coherence level of the adaptor stimulus and duration compression magnitude. However, increasing the motion coherence level in a stimulus also results in an increase in global speed. To test whether duration compression effects were driven by global speed or global motion, we repeated the experiment, but kept global speed fixed while varying motion coherence levels. The duration compression persisted, but the linear relationship with motion coherence was absent, suggesting that the effect was driven by adapting global speed mechanisms. Our results support previous claims that visual timing mechanisms persist at the level of global processing.
Data from: Resting-state gamma-band power alterations in schizophrenia reveal E/I-balance abnormalities across illness-stages
We examined alterations in E/I-balance in schizophrenia (ScZ) through measurements of resting-state gamma-band activity in participants meeting clinical high-risk (CHR) criteria (n = 88), 21 first episode (FEP) patients and 34 chronic ScZ-patients. Furthermore, MRS-data were obtained in CHR-participants and matched controls. Magnetoencephalographic (MEG) resting-state activity was examined at source level and MEG-data were correlated with neuropsychological scores and clinical symptoms. CHR-participants were characterized by increased 64–90 Hz power. In contrast, FEP- and ScZ-patients showed aberrant spectral power at both low- and high gamma-band frequencies. MRS-data showed a shift in E/I-balance toward increased excitation in CHR-participants, which correlated with increased occipital gamma-band power. Finally, neuropsychological deficits and clinical symptoms in FEP and ScZ-patients were correlated with reduced gamma band-activity, while elevated psychotic symptoms in the CHR group showed the opposite relationship. The current study suggests that resting-state gamma-band power and altered Glx/GABA ratio indicate changes in E/I-balance parameters across illness stages in ScZ.
Data from: Spatial patterns and interspecific associations among trees at different stand development stages in the natural secondary forests on the Loess Plateau, China
Quercus wutaishansea populations on the Loess Plateau are currently becoming more dominant in natural secondary forests, whereas Pinus tabulaeformis is declining. In the present paper, the diameter class (instead of age) was used to classify the different growth stages as juvenile, subadult, or adult, and the univariate function g(r) was used to analyze the dynamic changes in spatial patterns and interspecific associations in three 1‐ha tree permanent plots on the Loess Plateau, NW China. Our results suggested that the niche breadth changed with the development stage. The diameter distribution curve was consistent with the inverted "J" type, indicating that natural regeneration was common in all three plots. There was a close relationship between the spatial pattern and scale, which showed significant aggregation at small distances, and became more random as distance increased, but in the Pinus + Quercus mixed forests, the whole species were aggregated at distances up to 50 m. The degree of spatial clumping decreased from juvenile to subadult and from subadult to adult. The spatial pattern also differed at different growth stages, likely due to strong intraspecific competition. Associations among different growth stages were positively correlated at small scales. Our study is important to the understanding of the development of the Q. wutaishansea forests; thus, the spatial dynamic change features should be received greater attention when planning forest management and developing restoration strategies on the Loess Plateau.
Data from: Glutathione S-transferase protein expression in different life stages of zebrafish (Danio rerio)
Zebrafish is a widely used animal model in biomedical sciences and toxicology. Although evidence for the presence of phase I and phase II xenobiotic defense mechanisms in zebrafish exists on the transcriptional and enzyme activity level, little is known about the protein expression of xenobiotic metabolizing enzymes. Given the important role of glutathione S-transferases (GSTs) in phase II biotransformation, we analyzed cytosolic GST proteins in zebrafish early life stages and different organs of adult male and female fish, using a targeted proteomics approach. The established Multiple Reaction Monitoring-based assays enable the measurement of the relative abundance of specific GST isoenzymes and GST classes in zebrafish through a combination of proteotypic peptides and peptides shared within the same class. GSTs of the classes alpha, mu, pi and rho are expressed in zebrafish embryo as early as 4 hours post fertilization (hpf). The majority of GST enzymes are present at 72 hpf followed by a continuous increase in expression thereafter. In adult zebrafish, GST expression is organ dependent, with most of the GST classes showing the highest expression in the liver. The expression of a wide range of cytosolic GST isoenzymes and classes in zebrafish early life stages and adulthood supports the use of zebrafish as a model organism in chemical-related investigations.
Data from: Heat hardening capacity in Drosophila melanogaster is life stage specific and juveniles show the highest plasticity
Variations in stress resistance and adaptive plastic responses during ontogeny have rarely been addressed, despite the possibility that differences between life stages can affect species' range margins and thermal tolerance. Here, we assessed the thermal sensitivity and hardening capacity of Drosophila melanogaster across developmental stages from larval to the adult stage. We observed strong differences between life stages in heat resistance, with adults being most heat resistant followed by puparia, pupae and larvae. The impact of heat hardening (1 h at 35°C) on heat resistance changed during ontogeny, with the highest positive effect of hardening observed in puparia and pupae and the lowest in adults. These results suggest that immobile life stages (puparia and pupae) have evolved high plasticity in upper thermal limits whereas adults and larvae rely more on behavioural responses to heat stress allowing them to escape from extreme high temperatures. While most studies on the plasticity of heat resistance in ectotherms have focused on the adult life stage, our findings emphasize the crucial importance of juvenile life stages of arthropods in understanding the thermal biology and life stage-specific physiological responses to variable and stressful high temperatures. Failure to acknowledge this complication might lead to biased estimates of species' ability to cope with environmental changes, such as climate change.
Data from: The role of local ecology during hybridisation at the initial stages of ecological speciation in a marine snail
Hybrid zones of ecologically divergent populations are ideal systems to study the interaction between natural selection and gene flow during the initial stages of speciation. Here we perform an AFLP genome scan in parallel hybrid zones between divergent ecotypes of the marine snail Littorina saxatilis, which is considered a model case for the study of ecological speciation. RB (Ridged-Banded) and SU (Smooth-Unbanded) ecotypes are adapted to different shore levels and microhabitats, although they present a sympatric distribution at the mid-shore where they meet and mate (partially assortatively). We used shell morphology, outlier and non-outlier AFLP loci from RB, SU and hybrid specimens captured in sympatry to determine the level of phenotypic and genetic introgression. We found different levels of introgression at parallel hybrid zones and non-outlier loci showed more gene flow with greater phenotypic introgression. These results were independent from the phylogeography of the studied populations, but not from the local ecological conditions. Genetic variation at outlier loci was highly correlated with phenotypic variation. In addition, we used the relationship between genetic and phenotypic variation to estimate the heritability of morphological traits and to identify potential QTLs to be confirmed in future crosses. These results suggest that ecology (exogenous selection) plays an important role in this hybrid zone. Thus, ecologically-based divergent natural selection is responsible, simultaneously, for both ecotype divergence and hybridisation. On the other hand, genetic introgression occurs only at neutral loci (non-outliers). In the future, genome-wide studies and controlled crosses would give more valuable information about this process of speciation in the face of gene flow.
FIGURE 3 in A Taxonomic study of two species of Thiotricha Meyrick (Lepidoptera: Gelechiidae), from southwestern Japan, with notes on the biology of their immature stages
FIGURE 3. Female genitalia. Thiotricha gemmulans. Sclae bar: 0.40 mm.
FIGURE 2 in A Taxonomic study of two species of Thiotricha Meyrick (Lepidoptera: Gelechiidae), from southwestern Japan, with notes on the biology of their immature stages
FIGURE 2. Male genitalia. Thiotricha gemmulans. Scale bar: 0.20 mm.
Data from: Effects of temperature and drought on early life stages in three species of butterflies: mortality of early life stages as a key determinant of vulnerability to climate change?
Anthropogenic climate change poses substantial challenges to biodiversity conservation. Well-documented responses include phenological and range shifts, and declines in cold but increases in warm-adapted species. Thus, some species will suffer while others will benefit from ongoing change, although the biological features determining the prospects of a given species under climate change are largely unknown. By comparing three related butterfly species of different vulnerability to climate change, we show that stress tolerance during early development may be of key importance. The arguably most vulnerable species showed the strongest decline in egg hatching success under heat and desiccation stress, and similar pattern also for hatchling mortality. Research, especially on insects, is often focussed on the adult stage only. Thus, collating more data on stress tolerance in different life stages will be of crucial importance for enhancing our abilities to predict the fate of particular species and populations under ongoing climate change.
Data from: Effects of variation in resource acquisition during different stages of the life cycle on life-history traits and trade-offs in a burying beetle
Individual variation in resource acquisition should have consequences for life-history traits and trade-offs between them because such variation determines how many resources can be allocated to different life-history functions, such as growth, survival and reproduction. Since resource acquisition can vary across an individual's life cycle, the consequences for life-history traits and trade-offs may depend on when during the life cycle resources are limited. We tested for differential and/or interactive effects of variation in resource acquisition in the burying beetle Nicrophorus vespilloides. We designed an experiment in which individuals acquired high or low amounts of resources across three stages of the life cycle: larval development, prior to breeding and the onset of breeding in a fully crossed design. Resource acquisition during larval development and prior to breeding affected egg size and offspring survival, respectively. Meanwhile, resource acquisition at the onset of breeding affected size and number of both eggs and offspring. In addition, there were interactive effects between resource acquisition at different stages on egg size and offspring survival. However, only when females acquired few resources at the onset of breeding was there evidence for a trade-off between offspring size and number. Our results demonstrate that individual variation in resource acquisition during different stages of the life cycle has important consequences for life-history traits but limited effects on trade-offs. This suggests that, in species that acquire a fixed-sized resource at the onset of breeding, the size of this resource has larger effects on life-history trade-offs than resources acquired at earlier stages.
Data from: Impacts of drought and nitrogen addition on Calluna-heathlands differ with plant life-history stage
1. Climate change and atmospheric deposition of nitrogen (N) affect the biodiversity patterns and functions of ecosystems worldwide. While many single-factor studies have quantified ecosystem responses to single global change drivers, less is known about the interaction effects of these drivers on ecosystem functions. 2. Here, we present the results of a three-year field and a two-year greenhouse experiment, in which we assessed responses of Calluna vulgaris-heathlands to the single and combined effects of drought events (D) and N fertilisation (D: 25% precipitation reduction in the field experiment and 20-50% soil water content reduction in the greenhouse experiment; N fertilisation: 35 kg N ha−1 yr−1). 3. We examined the effects of D and N treatments on growth responses of the dominant dwarf shrub Calluna vulgaris (in terms of biomass production and allocation, tissue δ13C signatures and C:N ratios) in relation to two plant life-history stages and different 'ecotypes' (sub-Atlantic vs. subcontinental heathlands). 4. Plant responses varied strongly with life-history stage, and the interaction of N and D showed lower effects than would be expected based on additive responses to single factors. While D treatments had no effects on Calluna in the building phase (ca. ten-year-old plants), seedlings (particularly one-year-old plants) were highly susceptible to drought. Differences in response patterns were attributable to the high shoot-root ratios typical of young Calluna plants. These ratios decreased with progressing life-history as a result of increasing below-ground biomass investments. Below-ground biomass production and shoot-root ratios differed between plants from the different heathland sites. 5. Tissue δ13C signatures decreased and C:N ratios increased with plant age as a result of decreasing evaporative demands (per unit root biomass). N fertilisation increases the shoot-root ratios and thereby the drought susceptibility of Calluna plants. 6. Synthesis. Our findings suggest that plant responses to global change are difficult to anticipate by means of single-factor studies or by focusing on a single life-history stage. This highlights the need for global change research to include multiple factors and life-history stages when assessing an ecosystem's susceptibility to shifts in environmental conditions.
Data from: The accumulation of reproductive isolation in early stages of divergence supports a role for sexual selection
Models of speciation by sexual selection propose that male-female coevolution leads to the rapid evolution of behavioral reproductive isolation. Here, we compare the strength of behavioral isolation to ecological isolation, gametic incompatibility, and hybrid inviability in a group of dichromatic stream fishes. In addition, we examine whether any of these individual barriers, or a combined measure of total isolation, is predicted by body shape differences, male color differences, environmental differences, or genetic distance. Behavioral isolation reaches the highest values of any barrier and is significantly greater than ecological isolation. No individual reproductive barrier is associated with any of the predictor variables. However, marginally significant relationships between male color and body shape differences with ecological and behavioral isolation are discussed. Differences in male color and body shape predict total reproductive isolation between species; hierarchical partitioning of these two variables' effects suggests a stronger role for male color differences. Together, these results suggest an important role for divergent sexual selection in darter speciation but raise new questions about the mechanisms of sexual selection at play and the role of male nuptial ornaments.
Data from: Population genomics of a symbiont in the early stages of a pest invasion
Invasive species often depend on microbial symbionts, but few studies have examined the evolutionary dynamics of symbionts during the early stages of an invasion. The insect Megacopta cribraria and its bacterial nutritional symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in 2009. While M. cribraria was initially discovered on wild kudzu plants, it was found as a pest on soybeans within 1 year of infestation. Because prior research suggests Ishikawaella confers the pest status—that is, the ability to thrive on soybeans—in some Megacopta species, we performed a genomic study on Ishikawaella from US. Megacopta cribraria populations to understand the role of the symbiont in driving host plant preferences. We included Ishikawaella samples collected in the first days of the invasion in 2009 and from 23 locations across the insect's 2011 US range. The 0.75 Mb symbiont genome revealed only 47 fixed differences from the pest-conferring Ishikawaella in Japan, with only one amino acid change in a nutrition-provisioning gene. This similarity, along with a lack of fixed substitutions in the US symbiont population, indicates that Ishikawella likely arrived in the US capable of being a soybean pest. Analyses of allele frequency changes between 2009 and 2011 uncover signatures of both positive and negative selection and suggest that symbionts on soybeans and kudzu experience differential selection for genes related to nutrient provisioning. Our data reveal the evolutionary trajectory of an important insect-bacteria symbiosis in the early stages of an invasion, highlighting the role microbial symbionts may play in the spread of invasive species.
Data from: Genome-wide regulatory dynamics of translation in the Plasmodium falciparum asexual blood stages
The characterization of the transcriptome and proteome of Plasmodium falciparum has been a tremendous resource for the understanding of the molecular physiology of this parasite. However, the translational dynamics that link steady-state mRNA with protein levels are not well understood. In this study, we bridge this disconnect by measuring genome-wide translation using ribosome profiling, through five stages of the P. falciparum blood phase developmental cycle. Our findings show that transcription and translation are tightly coupled, with overt translational control occurring for less than 10% of the transcriptome. Translationally regulated genes are predominantly associated with merozoite egress functions. We systematically define mRNA 5′ leader sequences, and 3′ UTRs, as well as antisense transcripts, along with ribosome occupancy for each, and establish that accumulation of ribosomes on 5′ leaders is a common transcript feature. This work represents the highest resolution and broadest portrait of gene expression and translation to date for this medically important parasite.
Data from: Midbrain adaptation may set the stage for the perception of musical beat
The ability to spontaneously feel a beat in music is a phenomenon widely believed to be unique to humans. Though beat perception involves the coordinated engagement of sensory, motor, and cognitive processes in humans, the contribution of low-level auditory processing to the activation of these networks in a beat-specific manner is poorly understood. Here, we present evidence from a rodent model that midbrain pre-processing of sounds may already be shaping where the beat is ultimately felt. For the tested set of musical rhythms, on-beat sounds on average evoked higher firing rates than off-beat sounds, and this difference was a defining feature of the set of beat interpretations most commonly perceived by human listeners over others. Basic firing rate adaptation provided a sufficient explanation for these results. Our findings suggest that midbrain adaptation, by encoding the temporal context of sounds, creates points of neural emphasis that may influence the perceptual emergence of a beat.
Data from: Non-linear effects of phylogenetic distance on early-stage establishment of experimentally introduced plants in grassland communities
1. The phylogenetic distance of an introduced plant species to a resident native community may play a role in determining its establishment success. While Darwin's naturalization hypothesis predicts a positive relationship, the preadaptation hypothesis predicts a negative relationship. Rigorous tests of this now so-called Darwin's naturalization conundrum require not only information on establishment successes but also of failures, which is frequently not available. Such essential information, however, can be provided by experimental introductions. 2. Here, we analysed three datasets from two field experiments in Germany and Switzerland. In the Swiss experiment, alien and native grassland species were introduced as seeds only with and without disturbance (tilling). In the German experiment, alien and native grassland species were introduced both as seeds and as seedlings with and without disturbance (tilling), and with and without fungicide application. For the seedling introduction experiment, there was an additional herbivore-exclusion treatment. 3. Phylogenetic distance affected establishment in the three datasets differently, with success peaking at intermediate distances for the seed datasets, but decreasing with increasing distances in the seedling dataset. Disturbance favored seedling survival, most likely by weakening the resident community. 4. Synthesis: By analyzing experimental introductions, we show that the relationship between phylogenetic distance and establishment, at least for seedling emergence, may actually be non-linear with an optimum at intermediate distances. Therefore, Darwin´s naturalization hypothesis and the preadaptation hypothesis need not be in conflict. Rather, the mechanisms underlying them can operate simultaneously or alternately depending on the life stage and on the environmental conditions of the resident community.
Data from: Generation time, net reproductive rate, and growth in stage-age structured populations
Major insights into the relationship between life-history features and fitness have come from Lotka's proof that population growth rate is determined by the level (expected amount) of reproduction and the average timing of reproduction of an individual. But this classical result is limited to age-structured populations. Here we generalize this result to populations structured by stage and age by providing a new, unique measure of reproductive timing (Tc) that, along with net reproductive rate (R0), has a direct mathematical relationship to and approximates growth rate (r). We use simple examples to show how reproductive timing Tc and level R0 are shaped by stage dynamics (individual trait changes), selection on the trait, and parent-offspring phenotypic correlation. We also show how population structure can affect dispersion in reproduction among ages and stages. These macroscopic features of the life history determine population growth rate r and reveal a complex interplay of trait dynamics, timing, and level of reproduction. Our results contribute to a new framework of population and evolutionary dynamics in stage-and-age-structured populations.
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.