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.
2,135
datasets available to search
ShareScore release 0.9.0
Dataset results
2,135 results for “stabling”
Trophic ecology in an anchialine cave: a stable isotope study
Open the record for dataset details and reuse information.
Simulating the Water Balance of a Small Lake in the Subtropical Monsoon Region Based on Stable Isotopic Technique
Open the record for dataset details and reuse information.
APS DPP 2024 - The impact of stable modes on the merging dynamics of Kelvin- Helmholtz vortices
<p>Supplementary figures for the poster presentation</p>
Deep Learning for Structure-Preserving Universal Stable Koopman-Inspired Embeddings for Nonlinear Canonical Hamiltonian Dynamics
<p>This dataset provides python implementation of the paper: Deep Learning for Structure-Preserving Universal Stable Koopman-Inspired Embeddings for Nonlinear Canonical Hamiltonian Dynamics, which is available on arXiv https://arxiv.org/abs/2308.13835.</p>
A green solvent enables precursor phase engineering of stable formamidinium lead triiodide perovskite solar cells - Data Availability
<p>A green solvent enables precursor phase engineering of stable formamidinium lead triiodide perovskite solar cells - Data Availability</p>
AI-Assisted Restoration of Yangshao Painted Pottery Using LoRA and Stable Diffusion
<p>Images related to the paper *AI-Assisted Restoration of Yangshao Painted Pottery Using LoRA and Stable Diffusion* and the specially trained LoRA model for restoring Yangshao pottery patterns.</p>
Reproduction package for the paper "BH-BH mergers with & without EM counterpart: A model for stable tertiary mass transfer in hierarchical triple systems"
<p>This is a reproduction package for the paper "BH-BH mergers with & without EM counterpart: A model for stable tertiary mass transfer in hierarchical triple systems" by Kummer et al. (2024). It aims to provide the most important data products and reproduce the Figures of the paper.</p> <p> </p>
Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs
<div> <div> <h2>Abstract</h2> <a href="https://github.com/christabel-bucao/fish-variability-across-organs/#abstract"></a></div> <p>Phenotypic variation among individuals plays a key role in evolution, since variation provides the material on which natural selection can act. One important link between genetic and phenotypic variation is gene expression. As for other phenotypes, the range of accessible expression variation is limited and biased by different evolutionary and developmental constraints. Gene expression variability broadly refers to the tendency of a gene to vary in expression (i.e., between individuals or cells) due to stochastic fluctuations or differences in genetic, epigenetic, or environmental factors, separately from the differences between e.g. organs. Variability due to biomolecular stochasticity (transcriptional ‘noise’) and cell-to-cell heterogeneity has been well-studied in isogenic populations of unicellular organisms such as bacteria and yeasts. However, for more complex organisms with multiple cells, tissues, and organs sharing the same genetic background, the interplay between inter-individual expression variability, gene and organ function, and gene regulation remains an open question. In this study, we used highly multiplexed 3’-end Bulk RNA Barcoding and sequencing (BRB-seq) to generate transcriptome profiles spanning at least nine organs in outbred individuals of three ray-finned fish species: zebrafish, Northern pike, and spotted gar. For each condition, we measured expression variation per gene independent of mean expression level. We observed that lowly variable genes are enriched in cellular housekeeping functions whereas highly variable genes are enriched in stimulus-response functions. Furthermore, genes with highly variable expression between individuals evolve under weaker purifying selection at the coding sequence level, indicating that intra-species gene expression variability predicts inter-species protein sequence divergence. Genes that are broadly expressed across organs tend to be both highly expressed and lowly variable between individuals, whereas organ-biased genes are typically highly variable within their top organ of expression. For genes with organ-biased expression profiles, we inferred differences in selective pressure on gene regulation depending on their top organ. We found that genes with peak expression in the brain have low inter-individual expression variability across non-nervous organs, suggesting stabilizing selection on regulatory evolution of brain-biased genes. Conversely, liver-biased genes have highly variable expression across organs, implying weaker regulatory constraints. These patterns show that gene regulatory mechanisms evolved differently based on constraints on the primary organ.</p> <h2>Directory Structure</h2> </div> <ul> <li> <p><code>config/</code>: Contains YAML file indicating package versions for conda environment</p> </li> <li> <p><code>data/</code>: Contains input data</p> <ul> <li><code>counts/</code>: Contains counts and UMI-deduplicated counts. Currently under embargo and will be made available upon acceptance for publication.</li> <li><code>gene_metadata/</code>: Contains gene biotype information from Ensembl</li> <li><code>sample_metadata/</code>: Contains sample metadata files for each species</li> <li><code>selectome/</code>: Contains selection statistics from the <a href="https://selectome.org/" rel="nofollow">Selectome</a> database<br><br></li> </ul> </li> <li> <p><code>results/</code>: Contains output files sorted by subfolders labeled after each step of the analysis pipeline. Only R notebook HTML files are available on the Git repository, please check Zenodo for R data files.</p> <ul> <li><code>run_pipeline.Rdata</code>: Contains all parameters used for each step of the analysis pipeline<br><br></li> </ul> </li> <li> <p><code>workflow/</code>: Contains scripts used for the analysis pipeline</p> <ul> <li><code>analysis/</code>: Contains all steps of the analysis pipeline, available as .Rmd files</li> <li><code>functions/</code>: Contains all functions used for analysis/</li> <li><code>renv/</code>: Used for package management in R</li> <li><code>run_pipeline.R</code>: Runs all the steps under analysis/</li> <li><code>run_go_figure.sh</code>: Runs <a href="https://gitlab.com/evogenlab/GO-Figure" rel="nofollow">GO-Figure!</a> 1.0.0 (downloaded separately)</li> <li><code>demultiplex_brbseq_fastq.sh</code>: Used for demultiplexing BRB-seq fastq files using <a href="https://github.com/DeplanckeLab/BRB-seqTools">BRB-seqTools</a> 1.6.1 (downloaded separately) for uploading to NCBI SRA</li> <li><code>rename_fastq_files.sh</code>: Used for renaming demultiplexed fastq files by mapping each barcode to their corresponding sample name</li> <li><code>renv.lock</code>: Lockfile for managing R package versions. Run <code>renv::restore()</code> to set up the R environment based on packages specified in the lockfile. All package versions used are also specified in the output HTML files under results/.</li> </ul> </li> </ul> <div> <h2>Species Codes</h2> </div> <ul> <li><strong>LOC</strong>: <em>Lepisosteus oculatus</em> (spotted gar)</li> <li><strong>ELU</strong>: <em>Esox lucius</em> (Northern pike)</li> <li><strong>DRE</strong>: <em>Danio rerio</em> (zebrafish)</li> </ul>
Data from: Three-phase succession of autochthonous lactic acid bacteria to reach a stable ecosystem within seven days of natural bamboo shoot fermentation as revealed by different molecular approaches
Microbial community structure and population dynamics during spontaneous bamboo shoot fermentation for production of 'soidon' (indigenous fermented food) in North-east India were studied using cultivation-dependent and cultivation-independent molecular approaches. Cultivation-dependent analyses (PCR-amplified ribosomal DNA restriction analysis and rRNA gene sequencing) and cultivation-independent analyses (PCR-DGGE, qPCR and Illumina amplicon sequencing) were conducted on the time series samples collected from three independent indigenous soidon fermentation batches. The current findings revealed three-phase succession of autochthonous lactic acid bacteria to attain a stable ecosystem within 7 days natural fermentation of bamboo shoots. Weissella spp. (Weissella cibaria, uncultured Weissella ghanensis) and Lactococcus lactis subsp. cremoris predominated the early phase (1–2 days) which was joined by Leuconostoc citreum during the mid-phase (3 days), while Lactobacillus brevis and Lactobacillus plantarum emerged and became dominant in the late phase (5–7 days) with concurrent disappearance of W. cibaria and L. lactis subsp. cremoris. Lactococcus lactis subsp. lactis and uncultured Lactobacillus acetotolerans were predominantly present throughout the fermentation with no visible dynamics. The above identified dominant bacterial species along with their dynamics can be effectively utilized for designing a starter culture for industrialization of soidon production. Our results showed that a more realistic view on the microbial ecology of soidon fermentation could be obtained by cultivation-dependent studies complemented with cultivation-independent molecular approaches. Moreover, the critical issues to be considered for reducing methodological biases while studying the microbial ecology of traditional food fermentation were also highlighted with this soidon fermentation model.
Data from: Stable isotope signatures of underground seedlings reveal the organic matter gained by adult orchids from mycorrhizal fungi
1.Orchids produce dust seeds dependent on the provision of organic carbon by mycorrhizal fungi for their early development stages. Hence, all chlorophyllous orchids experience a dramatic switch in trophic strategies from initial mycoheterotrophy to either autotrophy or partial mycoheterotrophy during ontogeny. Yet, the degree to which partially mycoheterotrophic orchids gain carbon from their mycorrhizal fungi is unclear based on existing approaches. 2.Here, we propose a novel approach to quantify the fungal-derived organic matter gain of chlorophyllous mature orchids mycorrhizal with rhizoctonia fungi using the stable isotope signatures of their fully mycoheterotrophic (FMH) seedlings in a linear two-source mixing model. 3.We conducted a field germination experiment with seven orchid species and measured carbon, nitrogen and hydrogen stable isotope natural abundances and nitrogen concentrations of mature orchids, underground seedlings and autotrophic references. 4.After in situ burial for 19 – 30 months, germination rates varied considerably among five orchid species and failed for two. On average, underground seedlings were enriched in 13C and 15N relative to mature orchids and had higher nitrogen concentrations. Using the mean enrichment factors ε13C and ε2H of seedlings as FMH endpoint, the organic matter gain derived by mature orchids from mycorrhizas was ca. 20%. 5.Chlorophyllous orchids mycorrhizal with rhizoctonias are predisposed to partially mycoheterotrophic nutrition due to their initially mycoheterotrophic seedling stage. We show that the carbon and hydrogen isotope abundances of underground seedlings can be used in an improved mixing-model to identify a significant proportion of fungal-derived organic matter in mature orchids.
Data from: Revisiting comparisons of genetic diversity in stable and declining species: assessing genome-wide polymorphism in North American bumble bees using RAD sequencing
Genetic variation is of key importance for a species' evolutionary potential, and its estimation is a major component of conservation studies. New DNA sequencing technologies have enabled the analysis of large portions of the genome in nonmodel species, promising highly accurate estimates of such population genetic parameters. Restriction site-associated DNA sequencing (RADseq) is used to analyse thousands of variants in the bumble bee species Bombus impatiens, which is common, and Bombus pensylvanicus, which is in decline. Previous microsatellite-based analyses have shown that gene diversity is lower in the declining B. pensylvanicus than in B. impatiens. RADseq nucleotide diversities appear much more similar in the two species. Both species exhibit allele frequencies consistent with historical population expansions. Differences in diversity observed at microsatellites thus do not appear to have arisen from long-term differences in population size and are either recent in origin or may result from mutational processes. Additional research is needed to explain these discrepancies and to investigate the best ways to integrate next-generation sequencing data and more traditional molecular markers in studies of genetic diversity.
FIGURE 1 in Stable citations for herbarium specimens on the internet: an illustration from a taxonomic revision of Duboscia (Malvaceae)
FIGURE 1. Duboscia macrocarpa. The short, stout petiole and long, straight hairs on the petiole and stem can be clearly seen.
FIGURE 1 in Notes on Early Land Plants Today. 37. Towards a stable, informative classification of the Lepidoziaceae (Marchantiophyta)
FIGURE 1. Summary of phylogenetic relationships in the Lepidoziaceae. Only those groups strongly supported by molecular phylogenetic analyses are shown (Cooper et al. 2011, 2012) and all other relationships are collapsed to polytomies. Taxa that have not yet been included in a molecular phylogenetic study are indicated by dotted lines. Only Mastigopelma can be inserted in the phylogeny with any confidence. Thick grey bars indicate those groups whose representatives in the molecular phylogeny did not form supported monophyletic groups. Boxes are drawn around groups recognised in the interim classification. The uncertain status of Arachniopsis is indicated by placing it in parentheses alongside Telaranea. Telaranea and Arachniopsis have been considered synonyms, with Telaranea the conserved name (Engel & Smith Merrill 2002), but the types have not been included in phylogenetic analyses and it is unclear whether one or more genera will be necessary to accommodate the species here retained in Telaranea.
Meteorological, catchment wetness, natural tracers and stable isotopes of water data in Schwingbach Environmental Observatory, Germany
<p>Dataset includes the following high-resolution (3 h) variables in 2018 and 2019 :</p> <ul> <li>Meteorological data</li> <li>Discharge</li> <li>Soil moisture</li> <li>Water temperature</li> <li>pH</li> <li>Electrical conductivity</li> <li>stable isotopes of water</li> </ul>
Figure 1 in An ontogenetically stable sexual character in a montane agamid, Salea horsfieldii Gray, 1845 (Reptilia: Agamidae) from Nilgiris, India
Figure 1. Dimorphic secondary sexual ornamentation in different size classes of Salea horsfieldii. Insets a, b, c and d are females of SVL 28.6 mm, 36.2 mm, 57.2 mm and 71.4 mm, respectively, and e, f, g and h are males of SVL 29.08 mm, 40.6 mm, 67.4 mm and 74.7 mm, respectively. The red arrow mark shows the break at the nuchal region in males.
Figure 2 in An ontogenetically stable sexual character in a montane agamid, Salea horsfieldii Gray, 1845 (Reptilia: Agamidae) from Nilgiris, India
Figure 2. Histogram showing the frequency distribution of SVL (mm) in males (n = 170) on the left and females (n = 52) on the right.
Nickel and chromium stable isotopic composition of ureilites: implications for the Earth's core formation and differentiation of the ureilite parent body
<p>We report the first Ni and Cr stable isotope data for ureilite meteorites that are the mantle residue of a carbon-rich differentiated planet. Ureilites have similar Ni stable isotope compositions as chondrites, suggesting the core-mantle differentiation of ureilite parent body did not fractionate Ni isotopes. Since the size of Earth is potentially larger than that of ureilite parent body (UPB; with diameter > 690 km), resulting in higher temperatures at the core-mantle boundary of Earth, it can be predicted that the terrestrial core formation may not directly cause Ni stable isotope fractionation. On the other hand, we also report high-precision Cr stable isotope composition of ureilites, including one ureilitic trachyandesite (ALM-A) that is enriched in lighter Cr stable isotopes relative to the main-group ureilites, which suggests the partial melting occurred on UPB. The globally heavy Cr in the UPB compared to chondrites can be caused by sulfur-rich core formation processes.</p>
We are what we eat, plus some per mill: Using stable isotopes to estimate diet composition in Gyps vultures over space and time
<p><span><span><span><span><span><span><span><span><span><span><span>1. Dietary studies in birds of prey involve direct observation and examination of food remains at resting and nesting sites. Although these methods accurately identify diet in raptors, they are time consuming, resource intensive and associated with biases that stem from the feeding ecology of raptors like <i>Gyps </i>vultures (<i>Gyps africanus</i> and <i>Gyps rueppelli</i>). Our study set out to estimate diet composition in <i>Gyps </i>vultures informed by stable isotopes that provide a good representation of assimilated diet from carrion resources in local systems. </span></span></span></span></span></span></span></span></span></span></span></p> <p>2. We hypothesized that differences in <i>Gyps </i>vulture diet composition is a function of sampling location, and that these vultures move between Serengeti National Park and Selous Game Reserve to forage. We also, theorized that grazing ungulates are the principal items in <i>Gyps</i> vulture diet. </p> <p><span><span><span><span><span><span><span><span><span><span><span>3. Through a combination of linear and Bayesian models, diet derived from d<sup>13</sup>C in <i>Gyps</i> vultures consisted of grazing herbivores across study areas, with those in Serengeti National Park consuming higher proportions of grazing herbivores (> 87%). d<sup>13</sup>C differences in vulture feather subsets per site did not indicate vulture diet change, and in combination with blood d<sup>13</sup>C, vultures fed largely on grazers for ~159 days before they were sampled in both sites. Similarly, d<sup>15</sup>N values implied that <i>Gyps </i>vultures fed largely on herbivores across space and time. d<sup>34</sup>S ratios separated prey source for vultures between the two sites. d<sup>34</sup>S variation in vultures across sites resulted from differences in baseline (plant) d<sup>34</sup>S values, though it is not possible to match d<sup>34</sup>S to specific locations. </span></span></span></span></span></span></span></span></span></span></span></p> <p><span><span><span><span><span><span><span><span><span><span><span>4. Our findings highlight the relevance of repeated sampling that considers tissues with varying isotopic turnover and emerging Bayesian techniques for dietary studies using stable isotopes. Findings also suggested limited vulture movement between the two local systems. However, more sampling coupled with telemetry is required to fully comprehend this observation and its implications to <i>Gyps</i> vulture ecology and conservation.</span></span></span></span></span></span></span></span></span></span></span></p>
Engineering 'smart' viral RNA structures for stable and targeted siRNA delivery
<p>Innovative delivery strategies are needed in order to realize the potential of small interfering RNA (siRNA) in medicine. SiRNAs are short, double-stranded RNA molecules that silence genes by co-opting an endogenous RNA interference (RNAi) pathway. Because they act on messenger RNA (mRNA) sequences via RNAi, siRNAs hold promise as potentially curative therapies for genetic defects, autoimmune disorders, cancers, and other diseases that cannot be treated with traditional, protein-binding small molecule drugs and biologics. However, key physiological barriers largely have precluded the translation of siRNA drugs into clinical practice. <em>In vivo</em>, naked siRNAs are degraded rapidly by nucleases and cleared by the kidneys, resulting in a half-life of less than five minutes. Moreover, by comparison to small molecule drugs, siRNA drugs are relatively large, hydrophilic molecules that do not distribute widely to tissues or passively cross the cell membrane. Therefore, without an effective strategy for delivery, the accumulation of siRNA drugs at target sites is minimal. Today, there are few prominent siRNA delivery approaches, and each has significant limitations. For example, chemical modifications can improve nuclease resistance, but with the increase in stability also come tradeoffs in potency and safety. Lipid nanoparticles (LNPs) physically shield siRNAs from degradation and can be modified to promote biodistribution and uptake; but as LNPs are optimized for efficacy, they become increasingly complex, posing quality assurance, cost, and evaluation problems. Finally, conjugation to the <em>N</em>-Acetylgalactosamine (GalNAc) ligand is a promising delivery strategy for the liver, but targeted delivery to other tissues is a problem that still remains to be solved. Advances in nucleic acid nanotechnology have shown that RNA is an emerging platform for drug delivery. In particular, a three-way junction (3WJ) derived from bacteriophage prohead RNA (pRNA) has gained prominence as a vector for small molecule, microRNA (miRNA), anti-miRNA, and siRNA delivery. As a delivery solution for siRNA, RNA-based platforms like the pRNA 3WJ have many notable advantages. For example, size and shape can be controlled to minimize clearance, and functionalization with aptamers can drive cell uptake. Also, RNA is a fundamentally biocompatible molecule that is simple, straightforward to produce, and multifunctional. However, its metabolic instability is limiting. Exciting new research has uncovered 'smart' RNA structures that are produced by flaviviruses (<em>e.g.</em>, Zika, Dengue, West Nile) to thwart nuclease degradation. Compared to other RNA structures used for drug delivery, these nuclease-resistant structures (NRSs) may be uniquely positioned for <em>in vivo</em> applications. The aim of this project is to harness the inherent stability of flaviviral NRSs in the creation of a supramolecular platform for siRNA delivery. This project has the potential to address a critical need in the field of oligonucleotide therapeutics, which has few promising solutions for harnessing the power of RNAi in the clinic. Additionally, this project will validate new stable structures as building blocks for use in RNA nanotechnology and therefore will help researchers design supramolecular structures for a variety of applications well beyond those described in this proposal.</p>
Context dependent fitness costs of reproduction despite stable body mass costs in an Arctic herbivore
<p class="western">1. The cost of reproduction on demographic rates is often assumed to operate through changing body condition. Several studies have found that reproduction depresses body mass more if the current conditions are severe, such as high population densities or adverse weather, than under benign environmental conditions. However, few studies have investigated the association between the fitness and body mass costs of reproduction.</p> <p class="western">2. Using 25 years of individual-based capture-recapture data from Svalbard reindeer (<i>Rangifer tarandus platyrhynchus</i>), we built a novel Bayesian state-space model that jointly estimated inter-annual change in mass, annual reproductive success, and survival, while accounting for incomplete observations. The model allowed us to partition the differential effects of intrinsic and extrinsic factors on both non-reproductive mass change and the body mass cost of reproduction and to quantify their consequences on demographic rates.</p> <p class="western">3. Contrary to our expectation, the body mass cost of reproduction (mean = 5.8 kg) varied little between years (CV = 0.08) whereas the between-year variation in body mass changes, that were independent of the previous year's reproductive state, varied substantially (CV = 0.4) in relation to autumn temperature and the amount of rain-on-snow in winter. This mass loss led to a cost of reproduction on the next reproduction, which was amplified by the same environmental covariates, from a 10% reduction in reproductive success in benign years, to a 50% reduction in harsh years. The reproductive mass loss also resulted in a small reduction in survival.</p> <p class="western">4. Our results show how demographic costs of reproduction, driven by inter-annual fluctuations in individual body condition, result from the balance between body mass costs of reproduction and body mass changes that are independent of previous reproductive state. We illustrate how a strong context dependent fitness cost of reproduction can occur, despite a relatively fixed body mass cost of reproduction. This suggests that female reindeer display a very conservative energy allocation strategy, either aborting their reproductive attempt at an early stage or weaning at a relatively constant cost. Such a strategy might be common in species living in a highly stochastic food limited environment.</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.