Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,139
datasets available to search
ShareScore release 0.9.0
Dataset results
3,139 results for “fits”
Phenotype, genotype and fitness data related to genetic analysis of praziquantel response in schistosome parasites.
<p>These data are related to the study of the Genetic analysis of praziquantel response in schistosome parasites implicates a Transient Receptor Potential channel.</p> <p>Mass treatment with praziquantel (PZQ) monotherapy is the mainstay for schistosomiasis treatment. This drug shows imperfect cure rates in the field and parasites showing reduced PZQ response can be selected in the laboratory, but the extent of resistance in <em>Schistosoma mansoni</em> populations is unknown. We examined the genetic basis of variation in PZQ response in a <em>S. mansoni</em> population (SmLE-PZQ-R) selected with PZQ in the laboratory: 35% of these worms survive high dose (73 µg/mL) PZQ treatment. We used genome wide association to map loci underlying PZQ response. The major chr. 3 peak contains a transient receptor potential (Sm.TRPM_PZQ) channel (Smp_246790), activated by nanomolar concentrations of PZQ. PZQ response shows recessive inheritance and marker-assisted selection of parasites at a single Sm.TRPM_PZQ SNP enriched populations of PZQ-resistant (PZQ-ER) and sensitive (PZQ-ES) parasites showing >377 fold difference in PZQ response. The PZQ-ER parasites survived treatment in rodents better than PZQ-ES. Resistant parasites show 2.25-fold lower expression of Sm.TRPM_PZQ than sensitive parasites. Specific chemical blockers of Sm.TRPM_PZQ enhanced PZQ resistance, while Sm.TRPM_PZQ activators increased sensitivity. A single SNP in Sm.TRPM_PZQ differentiated PZQ-ER and PZQ-ES lines, but mutagenesis showed this was not involved in PZQ response, suggesting linked regulatory changes. We surveyed Sm.TRPM_PZQ sequence variation in 259 parasites from the New and Old World revealing one nonsense mutation that results in a truncated protein with no PZQ-binding site. Our results demonstrate that Sm.TRPM_PZQ underlies variation in PZQ response in <em>S. mansoni</em> and provides an approach for monitoring emerging PZQ-resistance alleles in schistosome elimination programs.</p> <p>This dataset is divided in 3 folders. Each folder has a readme detailing its content.</p> <p><strong>1-Phenotyping_data</strong></p> <p>This folder includes the data tables related to the phenotyping of the worms performed during this study. The phenotype measured was the viability of worms following PZQ treatment (i.e., PZQ response). This viability was assessed microscopically or using worm lactate production released in culture media.</p> <p>The data correspond to the following experiments:</p> <ul> <li>PZQ response of single adult male worms from SmLE and SmLE-PZQ-R populations to different doses of PZQ. This data was used to determine the PZQ IC50 of each population.</li> <li>Lactate production from single SmLE-PZQ-R adult male worms and correlation with visual observation. This was a proof-of-principle that lactate production can be used to efficiently and unbiasedly phenotype schistosome adult male worms in response to PZQ drug.</li> <li>PZQ response of single SmLE-PZQ-R adult male worms. These worms were then divided in low and high producer in response to PZQ and used to perform a genome-wide association study.</li> <li>PZQ response of single adult male worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations to different doses of PZQ. This data was used to determine the PZQ IC50 of each population.</li> <li>PZQ response of single adult male worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations in presence of Sm.TRPM_PZQ blocker (MB2) and activator (MV1) with and without PZQ drug.</li> <li>In vivo PZQ response of schistosome worms from SmLE-PZQ-ER and SmLE-PZQ-ES populations.</li> </ul> <p><strong>2-Genotyping_data</strong></p> <p>This folder includes the data tables related to the genotyping of the worms performed during this study. Worms were genotyping using PCR-RFLP (genotyping of single nucleotide polymorphisms (SNPs) on chr2 and chr3 QTLs) or using qPCR (genotyping of a copy number variation (CNV) on chr3 QTL).</p> <p>The data correspond to the following experiment:</p> <ul> <li>Association between PZQ response of single adult male worms from SmLE-PZQ-R population and their respective genotype on chromosome 2 (SNP) and chromosome 3 (SNP and CNV) loci.</li> </ul> <p><strong>3-Fitness_data</strong></p> <p>This folder includes the data tables related to the fitness of the parasite populations. We collected data regarding:</p> <ul> <li>The number of surviving and infected snails after exposure to SmLE-PZQ-ER or SmLE-PZQ-ES miracidia.</li> <li>The number of adult worms recovered from golden Syrian female hamsters exposed to SmLE-PZQ-ER or SmLE-PZQ-ES cercariae.</li> </ul> <p>All the data were collected during 12 generations of parasites and are used to evaluate a potential impact of PZQ resistance on the parasite fitness.</p>
Data from: Environmental conditions during development affect sexual selection through trait-fitness relationships
<p>Sexual selection can be shaped by spatial variation in environmental features among populations. Differences in sexual selection among populations generated through the effects of the environment could be shaped via four paths: differences in mean absolute fitness, differences in the means or variances of phenotypes, or differences in the absolute fitness-trait function relationship. Because sexual selection only occurs during the adult life stage, most studies have focused on identifying environmental features that influence these metrics of fitness and trait distributions among adults. However, these adult features could also be affected by environmental factors experienced in early life stages that then shape the trajectory for sexual selection during the adult life stage. Here we investigated how among-population variation in environmental conditions during the juvenile (larval) stage of two species of <i>Enallagma</i> damselflies shapes sexual selection on male body size. We found that environmental factors related to predation pressures, lake primary productivity, and habitat availability have a role in shaping spatial variation in sexual selection. This acts mainly through how the environment affects absolute fitness-body size associations, not spatial variation in mean fitness or body size means and variances. These results demonstrate that the underpinnings of sexual selection in the wild can arise from environmental conditions during pre-reproductive life stages.</p>
Dataset for: Effects of constant versus fluctuating temperatures on fitness indicators of the aphid Dysaphis plantaginea and the parasitoid Aphidius matricariae
<p>This is the dataset for the article entitled: Effects of constant versus fluctuating temperatures on fitness indicators of the aphid Dysaphis plantaginea and the parasitoid Aphidius matricariae.</p> <p>Like all organisms, insects encounter temperatures that fluctuate on different time scales: within a day, between days, or throughout the seasons. However, most studies on the impact of temperature on insect physiology, behaviour, morphology or ecology have focused on constant temperatures tested in the laboratory. In our study, we wanted to know if fluctuating temperatures during the day (7—17°C, average 12°C) can affect insects differently compared to a constant temperature of 12°C. We use as a model the apple aphid <em>Dysaphis plantaginea</em>, a major threat to apple orchards worldwide, and its parasitoid <em>Aphidius matricariae</em>, which is used in biological control. We found that many traits—but not all—were affected. In particular, the fluctuating thermal regime decreased the development time of aphids and parasitoids, improved the rate of parasitism, and tended (albeit slightly) to improve the survival of both species. In contrast, we did not find strong effects on morphological traits. Our results can be used to better predict how these agronomically important insects behave in orchards, how fluctuating temperatures affect host-parasitoid relationships, and ultimately what the implications are in the context of climate change and biological control.</p> <p> </p>
Text-fig. 3. Textures of main volcaniclastic deposits exposed in abandoned Ludvíkovice quarry. a: radial cracks surrounding some boulders (see arrows) in hot lahar deposit. b: jig-saw fit of fractures (see arrows) within a mega-block of debris-avalanche deposit. c: pseudo-fiamme texture of compacted argillized pumice-fall deposit. d: trachybasaltic lapilli-stone of phreato-magmatic eruption. e: palaeo-relief developed and buried within the pyroclastic unit. f: diagonal bedding in fluvial volcanigenic sandstones. g: diluted and fine-grained lahars embedded in volcanigenic sandstones. in A New Oligocene Flora From Ludvíkovice Near Děčín (České Středohoří Mts., The Czech Republic)
Text-fig. 3. Textures of main volcaniclastic deposits exposed in abandoned Ludvíkovice quarry. a: radial cracks surrounding some boulders (see arrows) in hot lahar deposit. b: jig-saw fit of fractures (see arrows) within a mega-block of debris-avalanche deposit. c: pseudo-fiamme texture of compacted argillized pumice-fall deposit. d: trachybasaltic lapilli-stone of phreato-magmatic eruption. e: palaeo-relief developed and buried within the pyroclastic unit. f: diagonal bedding in fluvial volcanigenic sandstones. g: diluted and fine-grained lahars embedded in volcanigenic sandstones.
Different measures of niche and fitness differences tell different tales
<p>In Modern Coexistence Theory, species coexistence can either arise via strong niche differences or weak fitness differences. Having a common currency for interpreting these mechanisms is essential for synthesizing knowledge across different studies and systems. However, several methods for quantifying niche and fitness differences exist, with little guidance on how and why these methods differ. Here, we first organize the available methods into three groups and review their differences from a conceptual point of view.Next, we apply four methods to quantify niche and fitness differences to one simulated and one empirical data set. We show that these methods do not only differ quantitatively, but affect how we interpret coexistence. Specifically, the different methods disagree on how resource supply rates (simulated data) or plant traits (empirical data) affect niche and fitness differences. We argue for a better theoretical understanding of what connects and sets apart different methods and more precise empirical measurements to foster appropriate method selection in coexistence theory.</p>
FIGURE 2 Fitted HeV urine pool prevalence and 95 in Ecological conditions predict the intensity of Hendra virus excretion over space and time from bat reservoir hosts
FIGURE 2 Fitted HeV urine pool prevalence and 95% confidence intervals from the most parsimonious GAMM with week, seasonal interactions with roost type and previous food shortages, and an adjustment for relative abundance of Pteropus alecto. Weekly data are overlaid, coloured by roost type, and sized by corresponding P. alecto relative abundance. Thin lines show the fitted curves from the random factor smooth including each roost per year
Data for: Atypical singing is associated with developmental stress and zero fitness in a male white-throated sparrow (Zonotrichia albicollis)
<p>Here we provide data for a manuscript in which we describe the atypical song of a male white-throated sparrow (<em>Zonotrichia albicollis</em>). We observed this male over multiple breeding seasons at our Cranberry Lake study site (Adirondack Mountains; New York; 44.15N, 74.78W). We recorded the male singing, and also made observations regarding his failure to obtain reproductive success. In addition, as the male was banded as a nestling, we were able to compare his morphometric measurements at the time to the population average. Our observations of this unique individual support a connection between developmental stress, atypical song, and fitness outcomes.</p>
Data from: Microgeographic variation in early fitness traits of Pinus sylvestris from contrasting soils
<p>Seedling phenotypic data from two Iberian <em>Pinus sylvestris</em><em> </em>provenances from contrasting soils (calcareous vs. siliceous) grown in a 3-year greenhouse experiment on both types of natural local substrate. Each line in the file corresponds to a different seedling. Phenotypic variables as described in the original paper published in American Journal of Botany, doi <a href="https://doi.org/10.1002/ajb2.16159">10.1002/ajb2.16159</a></p>
Acceptable loss: Fitness consequences of salinity-induced cell death in a halotolerant microalga
<p>Environmentally induced reductions in fitness components (survival, fecundity) are generally considered as passive, maladaptive responses to stress. However, there is also mounting evidence for active, programmed forms of environmentally induced cell death in unicellular organisms. While conceptual work has questioned how such programmed cell death (PCD) might be maintained by natural selection, few experimental studies have investigated how PCD influences genetic differences in longer-term fitness across environments. Here, we tracked the population dynamics of two closely related strains of the halotolerant microalga <em>Dunaliella salina</em>, following transfers across salinities. We showed that after a salinity rise, only one of these strains displayed a massive population decline (-69% in one hour), largely attenuated by exposure to a PCD inhibitor. However, this decline was followed by a rapid demographic rebound, characterized by faster growth than the non-declining strain, such that sharper decline was correlated with faster subsequent growth across experiments and conditions. Strikingly, the decline was more pronounced in conditions more favourable to growth (more light, more nutrients, less competition), further suggesting that it was not simply passive. We explored several hypotheses that could explain this decline-rebound pattern, which suggests that <span>successive stresses could select for </span>higher environmentally induced death in this system<span>.</span></p>
Detecting frequency-dependent selection through the effects of genotype similarity on fitness components
<p>Frequency-dependent selection (FDS) is an evolutionary regime that can maintain or reduce polymorphisms. Despite the increasing availability of polymorphism data, few effective methods are available for estimating the gradient of FDS from the observed fitness components. We modeled the effects of genotype similarity on individual fitness to develop a selection gradient analysis of FDS. This modeling enabled us to estimate FDS by regressing fitness components on the genotype similarity among individuals. We detected known negative FDS on the visible polymorphism in a wild <em>Arabidopsis</em> and damselfly by applying this analysis to single-locus data. Further, we simulated genome-wide polymorphisms and fitness components to modify the single-locus analysis as a genome-wide association study (GWAS). The simulation showed that negative or positive FDS could be distinguished through the estimated effects of genotype similarity on simulated fitness. Moreover, we conducted the GWAS of the reproductive branch number in <em>Arabidopsis thaliana</em> and found that negative FDS was enriched among the top-associated polymorphisms of FDS. These results showed the potential applicability of the proposed method for FDS on both visible polymorphism and genome-wide polymorphisms. Overall, our study provides an effective method for selection gradient analysis to understand the maintenance or loss of polymorphism.</p>
Prior choice and data requirements of Bayesian multivariate mixed effects models fit to tag-recovery data: The need for power analyses
<p>1. Recent empirical studies have quantified correlation between survival and recovery by estimating these parameters as correlated random effects with hierarchical Bayesian multivariate models fit to tag-recovery data. In these applications, increasingly negative correlation between survival and recovery has been interpreted as evidence for increasingly additive harvest mortality. The power of these hierarchal models to detect non-zero correlations has rarely been evaluated and these few studies have not focused on tag-recovery data, which is a common data type.</p> <p>2. We assessed the power of multivariate hierarchical models to detect negative correlation between annual survival and recovery. Using three priors for multivariate normal distributions, we fit hierarchical effects models to a mallard (<em>Anas</em> <em>platyrhychos</em>) tag-recovery dataset and to simulated data with sample sizes corresponding to different levels of monitoring intensity. We also demonstrate more robust summary statistics for tag-recovery datasets than total individuals tagged.</p> <p>3. Different priors lead to substantially different estimates of correlation from the mallard data. Our power analysis of simulated data indicated most prior distribution and sample size combinations could not estimate strongly negative correlation with useful precision or accuracy. Many correlation estimates spanned the available parameter space (–1,1) and underestimated the magnitude of negative correlation. Only one prior combined with our most intensive monitoring scenario provided reliable results. Underestimating the magnitude of correlation coincided with overestimating the variability of annual survival, but not annual recovery.</p> <p>4. The inadequacy of prior distributions and sample size combinations previously assumed adequate for obtaining robust inference from tag-recovery data represents a concern in the application of Bayesian hierarchical models to tag-recovery data. Our analysis approach provides a means for examining prior influence and sample size on hierarchical models fit to capture-recapture data while emphasizing transferability of results between empirical and simulation studies.</p>
M81 post-processed results from Lightning SED fitting
<p>The post-processed results from the Lightning SED fitting code as fit by the authors for the spatially resolved map of M81. The results are for the MCMC sampler (m81_map_mcmc.fits.gz) and the MPFIT minimizer (m81_map_mpfit.fits.gz). Fitting of this example was performed on a 32-core node of the Pinnacle cluster at the Arkansas High Performance Computing Center.</p>
Phenological mismatch affects individual fitness and population growth in the winter moth
<p>Climate change can severely impact species that depend on temporary resources by inducing phenological mismatches between consumer and resource seasonal timing. In the winter moth, warmer winters caused eggs to hatch before their food source, young oak leaves, became available. This phenological mismatch changed the selection on the temperature sensitivity of egg development rate. However, we know little about the fine-scale fitness consequences of phenological mismatch at the individual level and how this mismatch affects population dynamics in the winter moth. To determine the fitness consequences of mistimed egg hatching relative to timing of oak budburst, we quantified survival and pupation weight in a feeding experiment. We found that mismatch greatly increased mortality rates of freshly hatched caterpillars, as well as affecting caterpillar growth and development time. We then investigated whether these individual fitness consequences have population-level impacts by estimating the effect of phenological mismatch on population dynamics, using our long-term data (1994–2021) on relative winter moth population densities at four locations in the Netherlands. We found a significant effect of mismatch on population density with higher population growth rates in years with a smaller phenological mismatch. Our results indicate that climate change-induced phenological mismatch can incur severe individual fitness consequences that can impact population density in the wild.</p>
Data and code for: Failure to purge: Population and individual inbreeding effects on fitness across generations of wild Impatiens capensis
<p>Inbreeding exposes deleterious recessive alleles in homozygotes, lowering fitness and generating inbreeding depression (ID). Both purging (via selection) and fixation (via drift) should reduce segregating deleterious mutations and ID in more inbred populations. These theoretical predictions are not well-tested in wild populations, which is concerning given purging/fixation have opposite fitness outcomes. We examined how individual- and population-level inbreeding and genomic heterozygosity affected maternal and progeny fitness within and among 12 wild populations of <em>Impatiens capensis</em>. We quantified maternal fitness in home sites, maternal multilocus heterozygosity (using 12,560 SNPs), and lifetime fitness of selfed and predominantly outcrossed progeny in a common garden. These populations spanned a broad range of individual- (<span class="s1"><em>f</em></span><span class="s2"><sub>i</sub></span><em> </em>= -0.17–0.98) and population-level inbreeding (<span class="s1"><em>F</em></span><span class="s2"><sub>IS</sub></span> = 0.25–0.87). More inbred populations contained fewer polymorphic loci, less fecund mothers, and smaller progeny, suggesting higher fixed loads. However, despite appreciable ID (mean: 8.8 lethal equivalents per gamete), ID did not systematically decline in more inbred population. More heterozygous mothers were more fecund and produced fitter progeny in outcrossed populations, but this pattern unexpectedly reversed in highly inbred populations. These observations suggest that persistent overdominance or some other force acts to forestall purging and fixation in these populations.</p>
Datasets and R source code of manuscript "No evidence for an effect of chronic boat noise on the fitness of reared water fleas"
<p>Datasets and R source code of manuscript "No evidence for an effect of chronic boat noise on the fitness of reared water fleas"</p> <p>Experiments : exposition of Daphnia magna to boatnoise or silence along all their life. Measure of survival and clonal reproduction.</p>
Induction of Sis1 promotes fitness but not feedback in the heat shock response
<div class="page"> <div class="layoutArea"> <div class="column"> <p>The heat shock response (HSR) controls expression of molecular chaperones to maintain protein homeostasis. Previously, we proposed a feedback loop model of the HSR in which heat-denatured proteins sequester the chaperone Hsp70 to activate the HSR, and subsequent induction of Hsp70 deactivates the HSR. However, recent work has implicated newly synthesized proteins (NSPs) – rather than unfolded mature proteins – and the Hsp70 co-chaperone Sis1 in HSR regulation, yet their contributions to HSR dynamics have not been determined. Here we generate a new mathematical model that incorporates NSPs and Sis1 into the HSR activation mechanism, and we perform genetic decoupling and pulse-labeling experiments to demonstrate that Sis1 induction is dispensable for HSR deactivation. Rather than providing negative feedback to the HSR, transcriptional regulation of Sis1 by Hsf1 promotes fitness by coordinating stress granules and carbon metabolism. These results support an overall model in which NSPs signal the HSR by sequestering Sis1 and Hsp70, while induction of Hsp70 – but not Sis1 – attenuates the response.</p> </div> </div> </div>
Data and Code for Blaszczak et al. 2023, Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience
<p>Data and code for analyses in Blaszczak et al. 2023, Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience.</p> <p>See publication and ReadMe file for analysis description and further details. </p> <p>bioRxiv pre-print: Blaszczak, J.R., Yackulic, C., Shriver, R., & R.O. Hall, Jr. 2023. Models of underlying autotrophic biomass dynamics fit to daily river ecosystem productivity estimates improve understanding of ecosystem disturbance and resilience. https://doi.org/10.1101/2023.04.11.535773</p>
Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium
<p>Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically <span>embedded within complex multispecies communities and influenced by the environment, which can shape </span>costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR <em>in vivo</em> is limited. <span>To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (</span><em>Flavobacterium</em> <em>columnare</em><span>)</span> <span>in its fish host, capturing the effects of bacterial antibiotic resistance, multispecies coinfections</span> <span>(metazoan fluke </span><span><em>Diplostomum</em> <em>pseudospathaceum</em></span><span>), and antibiotic exposure. </span>We quantified real-time replication and virulence of sensitive and resistant bacteria and demonstrate that both bacteria can benefit from coinfection in terms of persistence and replication, depending on the coinfecting partner and antibiotic presence. We also show that antibiotics can benefit resistant bacteria by increasing bacterial replication under coinfection with flukes. These results emphasize the importance of diverse, inter-kingdom coinfection interactions and antibiotic exposure in shaping costs and benefits of AMR, supporting their role as significant contributors to the spread and long-term persistence of resistance.</p>
Data and code to reproduce analysis in Sacchi et al. 2023: Sex-specific fitness consequences of mate change in Scopoli's shearwaters (Calonectris diomedea)
<p>This data package contains data and code needed to reproduce the analysis reported in <strong>Sex-specific fitness consequences of mate change in Scopoli’s shearwaters (Calonectris diomedea), doi </strong>10.1016/j.anbehav.2023.05.017</p> <p>Included are:</p> <p>1) Readme file - description of all other files and variables described in datasets</p> <p>2) Appendix.Rmd = R code file containing all the analysis reported in the paper</p> <p>3) breed.txt = this data table contains data for the analysis of fitness/breeding success</p> <p>4) skip.txt = this data table contains data for the analysis of skipping behaviour</p> <p>5) females.txt = this file contains data in headed format to build CR models for the female population. Covariate indicates if an individual's life history started with event 1 (partner known, first partner) or with event 3 (partner unknown).</p> <p>6) males.txt = this file contains data in headed format to build CR models for the male population. Covariate indicates if an individual's life history started with event 1 (partner known, first partner) or with event 3 (partner unknown).</p> <p>7) gepat.pat = this file contains the matrix design necessary to run CR models with e-surge (version 2.2.3)</p> <p> </p>
Dataset and fitting methods for Kinetic Proofreading can Enhance Single Nucleotide Discrimination in a Non-enzymatic DNA Strand Displacement Network
<p>This upload contains raw experimental data and the fitting methods used for the article "Kinetic Proofreading can Enhance Single Nucleotide Discrimination in a Non-enzymatic DNA Strand Displacement Network".</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.