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12,683 results for “Tolerance”
Lab disease outcomes data evaluating how antibiotic tolerant vs. non-tolerant cell-free supernatant from Pseudomonas aeruginosa affects the interaction between a fungal pathogen (Batrachochytrium dendrobatidis) and amphibian (Rana sylvaticus), 2022.
Microbes living on hosts and in the environment can play a key role in helping hosts to combat pathogens. However, antibiotic-induced alterations to microbial metabolite production could disrupt this dynamic. Here, we investigated whether antibiotic tolerance influences the anti-pathogenic properties of host-associated (living on the host; biofilms) and environmental (living in the soil of water column; planktonic) microbes in vitro and in vivo. For our model host and pathogen, we used the amphibian (Rana sylvatica)-Batrachochytrium dendrobatidis (Bd) system. For our model host-associated (biofilm) and environmental (planktonic) microbes, we used four strains of Pseudomonas aeruginosa that vary in their tolerance to antibiotics and their biofilm-forming capabilities: Planktonic, non-antibiotic tolerant (ΔsagS/VC); Planktonic, antibiotic tolerant (ΔsagS::sagS_L154A); Biofilm, non-antibiotic tolerant (ΔsagS::sagS_D105A); Biofilm, antibiotic tolerant (ΔsagS::sagS). We collected cell-free supernatants (CFS) from each strain to examine the effects of metabolites. We conducted four experiments. In our pathogen-only exposures to test direct effects of metabolites on Bd, we exposed Bd zoospores to each P. aeruginosa CFS at six concentrations. After 11 days of growth, we measured relative abundance of Bd across each treatment. In our host-only exposures to test effects of metabolites on host disease outcomes, we placed R. sylvatica tadpoles in individual units containing each P. aeruginosa CFS. After 48 hours, water was changed into clean well water (no CFS). Bd zoospores were immediately added to each experimental unit following the water change. After 5 days of Bd exposure, we measured snout-vent length (SVL), mass, developmental stage, and Bd quantification in the mouthparts using qPCR for each tadpole. In our host-pathogen exposures to test interactive effects of metabolites on hosts in the presence of the pathogen, we conducted the same experiment as above. However, ins
Outdoor mesocosm study evaluating how mass, NaCl tolerance, and pesticide tolerance affect oxidative stress biomarkers (CAT, SOD, GR, GPx, TBARS) in larval wood frogs (Rana sylvatica) exposed to baseline and NaCl-contaminated conditions, 2019
Biomarkers of oxidative stress can aid in wildlife monitoring by allowing conservationists to detect sublethal environmental shifts. However, interpretation of stress responses can be complicated by multiple interacting factors (e.g., individual development, evolved physiological tolerance to stressors) which alter biomarker expression. Here, we investigated how individual ontogenetic traits and population-level tolerance traits influence oxidative stress responses under baseline and contaminated environmental conditions. For our model contaminant, we used NaCl (common freshwater contaminant due to factors such as coastal flooding, irrigation, airborne salt circulation, drought, runoff from road deicing salts). For our model wildlife populations, we used larval wood frogs (Rana sylvatica) from six noninteracting populations known to vary in two population-level tolerance traits: NaCl tolerance (calculated as average time to death from lethal NaCl exposure) and pesticide tolerance (determined by proxy of distance to agriculture - a consistent and highly repeatable relationship). At an outdoor research facility, R. sylvatica tadpoles were exposed to either baseline conditions (0 g/L NaCl added) or NaCl-contaminated conditions (1 g/L NaCl added for 21 days, then reduced to 0.5 g/L NaCl). Exposures were conducted in individual units with 40 replicates per population for each treatment. The experiment was terminated per individual to capture the full term of larval development (Developmental stage: Gosner stage 36), lasting between 33-48 days. For each individual, we measured mass, Snout-Vent-Length, and developmental stage before processing for biomarker expression. Individual homogenates were assayed for oxidative stress biomarkers superoxide dismutase (SOD; responsible for Reactive Oxygen Species capture and peroxide production), glutathione peroxidase (GPx; responsible for high-affinity peroxide reduction), catalase (CAT; responsible for low-affinity peroxide reducti
Supplementary Material for "Using Unstructured Crowd-sourced Data to Evaluate Urban Tolerance of Terrestrial Native Animal Species within a California Mega-City"
<p>This data repository is for the publication "Using Unstructured Crowd-sourced Data to Evaluate Urban Tolerance of Terrestrial Native Animal Species within a California Mega-City" and contains all R scripts and data files to reproduce results as well as all supplementary tables and figures.</p>
Transcriptomic atlas reveals organ-specific disease tolerance in sickle cell mice: dataset bone marrow HbAA mice injected or not with heme
<p>The objective of this experiment was to explore the transcriptome of the HbSS Townes mouse model of sickle cell disease. Townes model mice carry several human hemoglobin knock-in genes replacing the endogenous mouse genes and may be useful in studying sickle cell disease. All mice were genotyped, age- and sex-matched littermates. All HbAA (control, normal human hemoglobin) vs HbSS (sickle cell disease, mutated human hemoglobin) mice were used for experimentations at 6-8 weeks of age, to limit intra-group heterogeneity. Hemin (Ferriprotoporphyrin IX) was purchased from Frontiers Scientific and injected intravenously (iv.) in a retroorbital sinus at a concentration of 24 µmol/kg. Control mice received PBS instead. Mice were anesthetized with isoflurane 2-3% for injections, blood collection and sacrifice. All mice were sacrificed by cervical dislocation, 4 hours after injection.</p> <p>This dataset contains the results of the HbAA mice with and without heme.</p> <p>The corresponding HbSS mice with and without heme are deposited under number 10.5281/zenodo.10962782</p> <p>Bone marrow RNA was extracted by Macherey Nagel kit, according to the manufacturer’s instructions. The quality and quantity of mRNA were evaluated using a 2100<br>bioanalyzer with TNA 6000 NanoKits (all Agilent Technologies, Palo Alto, CA, USA). RNA Integrity Numbers superior to 7 were eligible for subsequent reverse transcription into cDNA. RNAseq was performed at the GenomIC plateform Cochin Institute INSERM U1016. After RNA extraction, RNA quality (RNA integrity number) was estimated. 1μg of high-quality total RNA sample (RIN &gt;7) was processed to build up the libraries, using TruSeq Stranded mRNA kit (Illumina) according to manufacturer instructions. Briefly, purified poly-A containing mRNA molecules were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during second strand synthesis allowed us to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of Illumina adapters.<br>Libraries were quantified by qPCR using KAPA Library Quantification Kits for Illumina Libraries (KapaBiosystems, Wilmington, MA). Library profiles were assessed using DNA High Sensitivity LabChip kits on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode. After sequencing, primary analysis based on AOZAN software (ENS, Paris), was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5).</p> <p>The dataset here represents 4 groups of mice, 4 mice per group as follows: HbAA PBS, HbAA heme, HbSS PBS, HbSS heme. </p> <p> </p>
Supplementary data for- Heat-evolved microalgae (Symbiodiniaceae) are stable symbionts and influence thermal tolerance of the sea anemone Exaiptasia diaphana
<p>Raw data and R codes for - Heat-evolved microalgae (Symbiodiniaceae) are stable symbionts and influence thermal tolerance of the sea anemone <em>Exaiptasia diaphana</em>. DOI: 10.1111/1462-2920.70011</p>
Within Population Variability of Coral Heat Tolerance - Images
<p>Image dataset used for a colour analysis of coral branches throughout a long-term marine heatwave emulation experiment using machine learning. Article: "Within population variability in coral heat tolerance indicates climate adaptation potential" by Humanes and Lachs et al. Code to analyse the dataset is found at 10.5281/zenodo.6256164.</p>
Non-genetically-based intraspecific differentiation for heavy metal tolerance in the copper moss Scopelophila cataractae
<p>We used next-generation sequencing to study DNA methylation and gene expression changes in plants from four clonal populations of the metallophyte moss <em>Scopelophila cataractae</em> experimentally exposed to either Cd or Cu. For this we performed reduced representation bisulfite DNA sequencing and RNA sequencing. </p>
Vertebrate DNA damage tolerance requires the C-terminus but not BRCT or transferase domains of REV1: Additional Files
<p>Additional information for Ross et al. (2005) Vertebrate DNA damage tolerance requires the C-terminus but not BRCT or transferase domains of REV1 published in Nucleic Acids Research Volume 33, Issue 4 doi:10.1093/nar/gki279, requested by an anonymous poster on PubPeer.</p> <p>A description of the individual files can be found in the README.txt file</p>
A Memristive Neural Decoder for Cryogenic Fault-Tolerant Quantum Error Correction - Syndromes Dataset
<p>Simulated sydromes measurement of quantum surface code error correction.<br>Used for the paper: "<a href="https://doi.org/10.48550/arXiv.2307.09463">A Memristive Neural Decoder for Cryogenic Fault-Tolerant Quantum Error Correction</a>".</p> <p>File names: <code>d-<surface_code_distance>_pfr-<physical_fault_rate>_nb-<number_of_samples></code></p> <p>Each file is formatted as csv with the following columns:</p> <ul> <li>label: binary label (0: no error, 1: error)</li> <li>syndromes: syndrome measurement sequence (tuples of the form (round, syndromes))</li> <li>quantity: number of samples for this label + syndrome sequence</li> </ul> <p>Only distance 3 is currently available with 10M samples for each physical fault rate.</p> <p>The data generation relies on <a href="https://github.com/quantumlib/Stim" target="_blank" rel="noopener">Stim</a>.</p>
A Memristive Neural Decoder for Cryogenic Fault-Tolerant Quantum Error Correction - Simulation Data
<p>Simulation output data used to generate figures of the paper: "<a href="https://doi.org/10.48550/arXiv.2307.09463">A Memristive Neural Decoder for Cryogenic Fault-Tolerant Quantum Error Correction</a>"</p>
Changes in gene expression during germination reveal pea genotypes with either 'quiescence' or 'escape' mechanisms of waterlogging tolerance
<p>Waterlogging causes germination failure in pea (<em>Pisum sativum</em> L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Among the most differentially regulated genes, upregulated gene tyrosine protein kinase responsible for metabolic regulation and downregulated LOX5 involved in fat metabolism indicated energy preservation in tolerant Kaspa, while in the other tolerant NL-2 subtilase family protein and PNC2 involved in protein and fat metabolism respectively showed upregulated expression suggesting energy utilization during waterlogging. By contrast, in sensitive genotype BM-3 high upregulation was recorded for the kunitz-type trypsin/protease inhibitor whose role is blocking the activity of protein metabolism leading to excessive lipid metabolism causing membrane leakage and subsequent seed damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea. </p>
Changes in gene expression during germination reveal pea genotypes with either 'quiescence' or 'escape' mechanisms of waterlogging tolerance
<p>Waterlogging causes germination failure in pea (<em>Pisum sativum</em> L.). Three genotypes (BM-3, NL-2 and Kaspa) contrasting in ability to germinate in waterlogged soil were exposed to different durations of waterlogging. Whole genome RNAseq was employed to capture differentially expressing genes. The ability to germinate in waterlogged soil was associated with testa colour and testa membrane integrity as confirmed by electrical conductivity measurements. Among the most differentially regulated genes, upregulated gene tyrosine protein kinase responsible for metabolic regulation and downregulated LOX5 involved in fat metabolism indicated energy preservation in tolerant Kaspa, while in the other tolerant NL-2 subtilase family protein and PNC2 involved in protein and fat metabolism respectively showed upregulated expression suggesting energy utilization during waterlogging. By contrast, in sensitive genotype BM-3 high upregulation was recorded for the kunitz-type trypsin/protease inhibitor whose role is blocking the activity of protein metabolism leading to excessive lipid metabolism causing membrane leakage and subsequent seed damage. Pathway analyses based on gene ontologies showed seed storage protein metabolism as upregulated in tolerant genotypes and downregulated in the sensitive genotype. Understanding the tolerance mechanism provides a platform to breed for adaptation to waterlogging stress at germination in pea. </p>
Data and code from: "Building multidimensional tolerance landscapes to predict the population dynamics of bacteria exposed to antibiotics in urban sewers"
<p>City sewers harbor diverse bacterial communities exposed to various antibiotic residues resulting from human consumption and excretion. Although these residues typically occur at sub-inhibitory concentrations, they can still impact the growth rate and yield of susceptible wastewater bacteria. Many bacteria exhibit antibiotic tolerance through transient phenotypic changes. Antibiotic residues, combined with complex environmental factors like temperature and salinity, especially in coastal cities, contribute to non-additive interactions that modulate antibiotic tolerance and affect population dynamics.</p> <p>To better understand these interactions, we developed continuous multivariate tolerance landscapes for three bacterial species: <strong><em><span>Escherichia coli</span></em></strong>, the emerging pathogen <strong><em><span>Streptococcus suis</span></em></strong>, and the sewer-inhabiting <strong><em><span>Arcobacter cryaerophilus</span></em></strong>. We modeled their intrinsic growth rates and carrying capacities across complex environments, incorporating temperature, salinity, and concentrations of two antibiotics (ciprofloxacin and azithromycin).<span> Using</span> these multivariate tolerance curves, we predicted microbial population dynamics in two sewers of Barcelona, highlighting the importance of environmental complexity in shaping microbial responses to antibiotic stressors.</p> <p> </p> <p><strong>Usage</strong></p> <p>Users can perform the analysis by running the R script (TC3D.R) after the installation of all</p> <p>package mentioned in the preamble,<span> </span></p> <p>This folder contains:</p> <p>- 3 datasets with OD measures for the 3 species:</p> <p><span> </span>* data_acrya.xlsx</p> <p><span> </span>* data_ecoli.xlsx</p> <p><span> </span>* data_ssuis.xlsx</p> <p>- 1 excel files with metadata (plate, well, species, environmental conditions)</p> <p><span> </span>* map_plate_all.xlsx</p> <p>- 4 datasets giving time series of the flow and several measures including <span> </span>conductivity and <span> </span>temperaturefor 2 sewers of Barcelona obtained from sample cabines <span> </span>set during the implementation of SCOREWATER (ID:820751)</p> <p><span> </span>* carmel_flow.csv</p> <p><span> </span>* carmel_quality.csv</p> <p><span> </span>* poblenou_flow.csv</p> <p><span> </span>* poblenou_quality.csv</p> <p>- 1 C++ script compiled and run with the R TMB package:</p> <p><span> </span>* fit_growth_r_K_SS_treatment.cpp : computes the negative loglikelihood for r and K, and state DOs, given the observed DO, for the populations under one same environmental treatment (salinity * temperature * antibiotic), and computes the density-dependence parameter alpha from r and K using the Delta Method.</p> <p><br><br></p>
Resource use strategies, resistance and tolerance to aerial biomass removal in Argentina mid-west native plants
<p>Dataset of the PhD Thesis from Lucas D. Gorné:<br> - Gorné LD. 2018. Estrategias de uso de recursos, resistencia y tolerancia a la remoción de biomasa aérea en plantas nativas del centro-oeste de Argentina. Tesis del Doctorado en Ciencias Biológicas. Facultad de Ciencias Exactas, Físicas y Naturales. Universidad Nacional de Córdoba. Córdoba, Argentina. https://ri.conicet.gov.ar/handle/11336/87925.</p>
Data from: Oxygen limited thermal tolerance is seen in a plastron breathing insect, and can be induced in a bimodal gas exchanger
<p>Dataset on respiration and ctmax in two freshwater bugs, associated with the paper:<br> <strong>Verberk WCEP & Bilton DT (2015) </strong>Oxygen limited thermal tolerance is seen in a plastron breathing insect, and can be induced in a bimodal gas exchanger. <em>Journal of Experimental Biology </em>218: 2083-2088. doi: 10.1242/jeb.119560</p>
Heterogeneous environmental seascape across a biogeographic break influences the thermal physiology and tolerances to ocean acidification in an ecosystem engineer
<p>Dataset for the metabolic rates of limpets under two different pCO2/pH conditions</p> <p>MR are in O2 mg h−1g−1</p>
Inducible tolerance to agrochemicals was paved by evolutionary responses to predators.
These are survival data of larval wood frogs (Lithobates sylvaticus) exposed to 7 sublethal treatments, followed by an exposure to a lethal insecticide treatment to see if tolerance can be rapidly induced. The data are associated with a journal article in Environmental Science and Technology, 2017, 51:13913-13919.
Drought increases microbial allocation to stress tolerance but with few tradeoffs among community-level traits
Climate change will increase soil drying, altering microbial communities via increasing water stress and decreasing resource availability. The responses of these microbial communities to changing environments is likely governed by physiological tradeoffs between high yield, resource acquisition, and stress tolerance (Y-A-S framework). We leveraged a unique field experiment that manipulates both drought and carbon availability across two years and three land uses, and we used both metagenomic and bioassay indicators of the three microbial community traits to test the following hypotheses: 1. Drought increases microbial allocation to stress tolerance functions, at the expense of growth and resource acquisition. 2. Because microbes are resource-limited under drought, increased carbon will enable greater expression of stress tolerance. 3. All three key life history traits described in the YAS framework will trade off, especially when resources are limited. Drought did increase microbial physiological investment in stress tolerance (measured via trehalose production), but we saw few other changes in microbial communities under drought. Carbon addition increased resource acquisition (measured via enzyme activity and resource acquisition gene abundance) and stress tolerance (trehalose assay), but did so in both drought and average rainfall environments. We found no evidence of trait tradeoffs, as we found no significant negative correlations between traits (measured via bioassay and metagenomics). In summary, we found C addition, and to a lesser extent, drought, both altered microbial community function and functional genes. However, resources did not alter drought response in a way that was consistent with theory of life history tradeoffs.
Fig. 1 in Temperature affects the hypoxia tolerance of neotropical Cichlid Geophagus brasiliensis
Fig. 1. Malate Dehydrogenase enzyme activity of Geophagus brasiliensis exposed to normoxic (90% oxygen saturation) and hypoxia (20% oxygen saturation) conditions for 8 hours at 20°C, 24°C and 28°C. a. in liver; b. in white muscle; and c. in heart. Asterisks indicates significant differences between treatments at the same temperature, p <0.05. Different lowercase letters indicate significant differences for the same treatment at the temperatures studied, p <0.05.
Fig. 3 in Temperature affects the hypoxia tolerance of neotropical Cichlid Geophagus brasiliensis
Fig. 3. Citrate Synthase enzyme activity of Geophagus brasiliensis exposed to normoxic (90% oxygen saturation) and hypoxic (20% oxygen saturation) conditions for 8 hours at 20°C, 24°C and 28°C. a. in liver; b. in white muscle; and c. in heart. Asterisks indicates significant differences between treatments at the same temperature, p <0.05. Different lowercase letters indicate significant differences for the same treatment at the temperatures studied, p <0.05.
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