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.
122
datasets available to search
ShareScore release 0.9.0
Dataset results
122 results for “structural stability”
Fig. 6. nMDS analysis during high waters and low waters. a and b in Stability and spatio-temporal structure in fish assemblages of two floodplain lagoons of the lower Orinoco River
Fig. 6. nMDS analysis during high waters and low waters. a and b = gill nets sampling; c and d = seine net sampling. Each symbol represents one sample, filled symbols belongs to Las Arhuacas (arh) and those of open symbols to Los Cardonales (car). The dissimilarity between the sampling is approximately proportional to the distance, that is to say to greater distance greater dissimilarity. The abbreviations of the habitats are explained in the Fig. 2.
Fig. 2 in Stability and spatio-temporal structure in fish assemblages of two floodplain lagoons of the lower Orinoco River
Fig. 2. Percentage distribution abundance and biomass of fish by habitats in each hydrological phase in both lagoons. DW = Descent water, LW = Low water, RW = Raise water and HW = High water. RO = Rocky outcrops, FGF = Flooded grass fields, FF = Floodplain forests, B = Beach, AV = Aquatic vegetation, LZFT = Littoral zone with fallen trunks and LZOW = Littoral zone and open waters.
Speciation and Structures in Pt Surface Sites Stabilized by N-Heterocyclic Carbene Ligands Revealed by DNP Enhanced Indirect-ly Detected 195Pt NMR Spectroscopic Signatures and Fingerprint Analysis
<p>Raw NMR data for the paper published under DOI: 10.1021/jacs.2c08300</p>
Relaxation effects in twisted bilayer molybdenum disulfide: structure, stability, and electronic properties
<p><strong>Abstract</strong></p> <p>Manipulating the interlayer twist angle is a powerful tool to tailor the properties of layered two-dimensional crystals. The twist angle has a determinant impact on these systems' atomistic structure and electronic properties. This includes the corrugation of individual layers, formation of stacking domains and other structural elements, and electronic structure changes due to the atomic reconstruction and superlattice effects. However, how these properties change with the twist angle, <em>θ</em>, is not yet well understood. Here, we monitor the change of twisted bilayer (tBL) MoS<sub>2</sub> characteristics as a function of <em>θ</em>. We identify distinct structural regimes, each with particular structural and electronic properties. We employ a hierarchical approach ranging from a reactive force field through the density-functional-based tight-binding approach and density-functional theory. To obtain a comprehensive overview, we analyzed a large number of tBLs with twist angles in the range of <span class="math-tex">\(\theta=0.2^\circ\dots59.6^\circ\)</span>. Some systems include up to half a million atoms, making structure optimization and electronic property calculation challenging. For <span class="math-tex">\(13^\circ \lessapprox \theta \lessapprox 47^\circ\)</span>, the structure is well-described by a moiré regime composed of two rigidly twisted monolayers. At small twist angles (<span class="math-tex">\(\theta\leq3^\circ\)</span> and <span class="math-tex">\(57^\circ\leq\theta\)</span>), a domain-soliton regime evolves, where the structure contains large triangular stacking domains, separated by a network of strain solitons and short-ranged high-energy nodes. The corrugation of the layers and the emerging superlattice of solitons and stacking domains affects the electronic structure. Emerging predominant characteristic features are Dirac cones at <em>K</em> and kagome bands. These features flatten for <em>θ</em> approaching 0<sup>∘</sup> and 60<sup>∘</sup>. Our results show at which range of <em>θ</em> the characteristic features of the reconstruction, namely extended stacking domains, the soliton network, and superlattice, emerge and give rise to exciting electronics. We expect our findings also to be relevant for other tBL systems.</p> <p>DOI: 10.1088/2053-1583/aceb75</p> <p><strong>Overview</strong></p> <p>This repository contains calculation files, optimized structures, and visualization movies for studies of twisted-bilayer MoS<sub>2</sub>, focussing on structural properties and electronic structure. Each directory has its own README.md file with additional information, separated by what data is included and the method used.</p> <p><strong>Geometry optimization</strong></p> <ul> <li>Directory `calc_structure_optimization_ReaxFF`: calculation files of the structure optimization of all studied structures, done with ReaxFF.</li> <li>Directory `calc_structure_optimization_DFT`: validation calculation files of the ReaxFF-optimized structures using DFT optimization.</li> </ul> <p><strong>Electronic structure calculations</strong></p> <ul> <li>Directory `calc_electronic_properties_DFT`: calculation files of electronic structure calculations on the DFT level.</li> <li>Directory `calc_electronic_properties_DFTB`: calculation files of electronic structure calculations on the DFTB level</li> </ul> <p><strong>Results</strong></p> <ul> <li>Directory `structures_rigidly_twisted`: structure files in cif format of the rigidly twisted (flat) systems, labeled by their twist angle.</li> <li>Directory `structures_fully_optimized`: structure files in cif format of the fully ReaxFF-optimized systems, labeled by their twist angle.</li> <li>Directory `movies`: visualization of the change of the interlayer distance landscape and the strain fields with the twist angle.</li> <li>Additionally, the script `plot_interlayer_distance.py` is included, which was used to create the individual frames of the movie showing the interlayer distance.</li> </ul>
Changes in vertical and horizontal diversities mediated by the size structure of introduced fish collectively shape food-web stability
<p><span>Species introductions can alter local food-web structure by changing the vertical or horizontal diversity within communities, largely driven by their body size distributions. Increasing vertical and horizontal diversities is predicted to have opposing effects on stability. However, their interactive effects remain largely overlooked. We investigated the independent and collective effects of vertical and horizontal diversities on food-web stability</span><span> in alpine lakes stocked with variable body size distributions of introduced fish species. I</span><span>ntroduced predators destabilize food-webs by </span><span>increasing vertical diversity through food chain lengthening</span><span>. Alternatively, increasing horizontal diversity results in more </span><span>stable food-web topologies. A non-linear interaction between vertical and horizontal diversities </span>suggests that increasing vertical diversity is most destabilizing when horizontal diversity is low<span>.</span> <span>Our findings suggest </span>that the size structure of introduced predators drives their impacts on stability by modifying the structure of food-webs, and highlights the <span>interactive effects of vertical and horizontal diversities on stability.</span></p>
FireProtDB + PDB Structural Protein Stability Dataset
<p>Dataset compiled and curated for use in the ThermoMPNN paper: <a href="https://doi.org/10.1073/pnas.2314853121">https://doi.org/10.1073/pnas.2314853121</a>: </p> <p>Dataset for training models for prediction of thermodynamic stability changes (ddG) of protein point mutations given a wildtype protein structure (PDB) file. Data was assembled by matching sequence-based ddG measurements in <a href="https://loschmidt.chemi.muni.cz/fireprotdb/">FireProtDB</a> to structures from the <a href="https://www.rcsb.org/">RCSB Protein Data Bank </a>(PDB). For details, see the Methods section of our manuscript.</p> <p>Citing this work: If you choose to use this dataset for your own research, please cite this repository and the ThermoMPNN paper: <a href="https://doi.org/10.1073/pnas.2314853121">https://doi.org/10.1073/pnas.2314853121</a>.</p> <p> </p> <p>Contents:</p> <p>pdbs/ directory contains all PDB files</p> <p>csvs/ directory contains all CSVs with mutation data</p> <p>csvs/4_fireprotDB_bestpH.csv is the main (full) dataset file with 3,438 mutations across 100 proteins.</p> <p>csvs/fireprot_splits.pkl contains the dataset splits (train/val/test) used in our study</p> <p>csvs/splits/ contains csvs for each of the splits (train/val/test/homologue-free) indexed from the full dataset csv.</p> <p>Important CSV columns:</p> <ul> <li>pdb_id_corrected: corresponds to the PDB in the pdbs/ directory (after curation and disambiguation)</li> <li>ddG: ddG value for mutation (mutant - WT)</li> <li>wild_type: wild-type amino acid (1-letter code)</li> <li>mutation: mutant amino acid (1-letter code)</li> <li>pdb_position: 0-based index of the mutated residue in the PDB file (may be different from position in the original FireProtDB sequence entry)</li> </ul> <p> </p>
Site-specific structure and stability constrained substitution models improve phylogenetic inference
Open the record for dataset details and reuse information.
Changes in vertical and horizontal diversities mediated by the size structure of introduced fish collectively shape food-web stability
Open the record for dataset details and reuse information.
Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks
Open the record for dataset details and reuse information.
Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure
We examined the hypothesis that genetics-based interactions between strongly interacting foundation species, the tree Populus angustifolia and the aphid Pemphigus betae, affect arthropod community diversity, stability and species interaction networks of which little is known. In a 2-year experimental manipulation of the tree and its aphid herbivore four major findings emerged: (i) the interactions of these two species determined the composition of an arthropod community of 139 species; (ii) both tree genotype and aphid presence significantly predicted community diversity; (iii) the presence of aphids on genetically susceptible trees increased the stability of arthropod communities across years; and (iv) the experimental removal of aphids affected community network structure (network degree, modularity and tree genotype contribution to modularity). These findings demonstrate that the interactions of foundation species are genetically based, which in turn significantly contributes to community diversity, stability and species interaction networks. These experiments provide an important step in understanding the evolution of Darwin's 'entangled bank', a metaphor that characterizes the complexity and interconnectedness of communities in the wild.
Data for: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks
<p>The persistence of mutualisms is paradoxical, as there are fitness incentives for exploitation. This is particularly true for plant-microbe mutualisms like arbuscular mycorrhizae (AM), which are promiscuously horizontally-transmitted. Preferential allocation by hosts to the best mutualist can stabilize horizontal mutualisms, however, preferential allocation is imperfect, with its fidelity likely depending upon the spatial structure of symbionts in plant roots. In this study, we tested AM mutualisms' dependence on two dimensions of spatial structure: the initial spatial association of fungi and the ease of fungal dispersal, through three complementary experiments. We found that fitness of the beneficial AM fungus increased when fungi were initially separate, while initial spatial mixing benefited the fitness of the non-beneficial fungus. These effects were strongest when dispersal was limited, and hosts could discriminate. Additionally, we found that changes in AM fungal proportional abundance induced by spatial structure in roots of a preferentially allocating host produced positive feedbacks on plant growth, showing that interactions between spatial structure and host choice can determine the direction of plant-soil feedbacks. Our results suggest that symbiont spatial structure within plant roots may act as an important modifier of plant preferential allocation and the dynamics of mycorrhizal mutualisms, with potentially cascading effects on plant-plant interactions.</p>
Core-shell structured chitosan-polyethylenimine nanoparticles for gene delivery: Improved stability, cellular uptake, and transfection efficiency
<p>Gene therapy has emerged as a promising treatment option for various acquired and inherited diseases. The delivery of nucleic acids relies on so-called vectors that condense and encapsulate their cargo, generating stable nano-sized particles. Especially non-viral gene delivery systems are of increasing interest. However, accomplishing therapeutic levels of transgene expression and limited tolerability of these systems remain a challenge. Therefore, we investigate in the present study the improvement of nucleic acid delivery using depolymerized chitosan – polyethylenimine DNA core complexes (dCS-PEI/DNA). These core complexes are further entrapped into a variety of dCS-based shells, functionalized with poly(ethylene glycol) (PEG) spacers conjugated to ionic moieties (amino or carboxylate groups) and cell penetrating peptides. This modular approach allowed to evaluate the effect of the shell functional components on the physico-chemical particle characteristics and biological effects <em>in vitro</em>. The optimized ternary complex combines a core-dCS-LPEI/DNA complex with a shell consisting of dCS-PEG-COOH, which resulted in improved encapsulation of nucleic acid, accelerated cellular uptake, enhanced transfection efficiency, and superior transfection potency in human hepatoma HuH-7 cells and mouse primary hepatocytes. Effects on transgene expression are confirmed <em>in vivo</em> in wild-type mice following retrograde intrabiliary infusion. After administration to mice of only 100 ng complexed nanovector DNA, ternary complexes induce a high reporter gene signal for three days. We conclude that ternary core-shell structured particles comprising functionalized chitosan are a promising gene delivery technology for both <em>in vitro</em> as well as <em>in vivo </em>applications. The modular design will facilitate the development of chemically modified derivatives.</p>
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels - full trajectories of SaFabI and EcFabI monomers and G112/113V mutants
<p>The following IDs are related to trajectories:</p> <p>v36 = EcFabI apo, monomer<br> v42 = EcFabI + TCL complex, monomer<br> v43 = EcFabI + MUT complex, monomer<br> v44 = EcFabI + AFN complex, monomer<br> v35 = SaFabI apo, monomer<br> v45 = SaFabI + TCL complex, monomer<br> v46 = SaFabI + MUT complex, monomer<br> v47 = SaFabI + AFN complex, monomer<br> v52 = G112V EcFabI apo, tetramer<br> v53 = G112V EcFabI apo, monomer<br> v54 = G113V SaFabI apo, tetramer<br> v55 = G113V SaFabI apo, monomer</p>
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels - full trajectories of SaFabI and EcFabI tetramers
<p>The following IDs are related to trajectories:</p> <p>v1 = EcFabI apo, tetramer<br> v2 = EcFabI + TCL complex, tetramer<br> v3 = EcFabI + MUT complex, tetramer<br> v39 = EcFabI + AFN complex, tetramer<br> v16 = SaFabI apo, tetramer<br> v17 = SaFabI + TCL complex, tetramer<br> v18 = SaFabI + MUT complex, tetramer<br> v40 = SaFabI + AFN complex, tetramer</p>
Do Go Chasing Waterfalls: Enoyl Reductase (FabI) in Complex with Inhibitors Stabilizes the Tetrameric Structure and Opens Water Channels - trajectories employed in Markov State Models and water analyses
<p>The following trajectories were employed in the generation of MSM models and water analyses:</p> <p>SaFabI_60us_align.zip</p> <p>EcFabI_60us_align.zip</p> <p>waters_SaFabI.tar.gz</p> <p>waters_EcFabI.tar.gz</p>
Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees
<p><span>Spatial patterns of biodiversity in the Atlantic Forest of Brazil are well characterized. However, there is no consensus on the biological processes underlying these patterns, and multiple competing hypotheses have been proposed, several of which center on climatic stability. Here, we ask if Late Quaternary climatic stability predicts contemporary population structure and genomic-level diversity in two palm species: </span><span>Syagrus botryophora </span><span>and S. pseudococos (Arecaceae)</span></p> <p><span>We first use species occurrence data to model the distribution of suitable environments in 62 time-slice climate projections over the last 120 thousand years, and summarize stability over that period. We then use >25,000 RADseq-generated SNPs to i) describe the spatial patterns of genomic variation in both species, ii) test how well genomic variation is explained by isolation by distance and by the environmental resistance imposed by historical instability (isolation by resistance) and iii) test for a correlation between genetic diversity and historical stability.</span></p> <p><span>The contemporary range of S. botryophora has been relatively stable over the last 30 thousand years and there are two isolated regions of high stability for S. pseudococos. The genomic data recovers a clear pattern of isolation by distance in S. botryophora and two structured populations in S. pseudococos. Consequently, the contribution of isolation by resistance to overall genetic structure is much higher in S. pseudococos. Genetic diversity is not significantly correlated with historical stability in either species.</span></p> <p><span>Based on the concordance between historical stability and genetic structure, Late Quaternary climate stability may have maintained population connectivity within S. botryophora and promoted intraspecific divergence in S. pseudococos. Conversely, historical stability does not seem to be driving spatial patterns of genetic diversity. This study supports the primary role of climatic stability in determining spatial population structure, but not genetic diversity, in the Atlantic Forest.</span></p>
Data for "Structure, short-range order, and phase stability of the Al$_x$CrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis"
<p>Data associated with "Structure, short-range order, and phase stability of the AlxCrFeCoNi high-entropy alloy: Insights from a perturbative, DFT-based analysis", published in npj Comput. Mater. <strong>10</strong>, 271 (2024).</p>
On the structure of the drifton phase space and its relation to the Rayleigh–Kuo criterion of the zonal-flow stability
<p>These are the supplementary data that can be used to generate figure 3, 4, and 5 in the manuscript "On the structure of the drifton phase space and its relation to the Rayleigh--Kuo criterion of the zonal-flow stability". The abstract of this manuscript reads as follows:</p> <p>The phase space of driftons (drift-wave quanta) is studied within the generalized Hasegawa--Mima collisionless-plasma model in the presence of zonal flows. This phase space is made intricate by the corrections to the drifton ray equations that were recently proposed by Parker [J. Plasma Phys. 82, 595820602 (2016)] and Ruiz et al. [Phys. Plasmas 23, 122304 (2016)]. Contrary to the traditional geometrical-optics (GO) model of the drifton dynamics, it is found that driftons can be not only trapped or passing, but they can also accumulate spatially while experiencing indefinite growth of their momenta. In particular, it is found that the Rayleigh--Kuo threshold known from geophysics corresponds to the regime when such "runaway" trajectories are the only ones possible. On one hand, this analysis helps visualize the development of the zonostrophic instability, particularly its nonlinear stage, which is studied here both analytically and through wave-kinetic simulations. On the other hand, the GO theory predicts that zonal flows above the Rayleigh--Kuo threshold can only grow; hence, the deterioration of intense zonal flows cannot be captured within a GO model. In particular, this means that the so-called tertiary instability of intense zonal flows cannot be adequately described within the quasilinear wave kinetic equation, contrary to some previous studies.</p>
Effect of Presodiation Additive on Structural and Interfacial Stability of Hard Carbon | P2-Na0.66Mn0.75Ni0.2Mg0.05O2 Full Cell
Open the record for dataset details and reuse information.
Seasonality and inter-annual stability in the population genetic structure of Batrachospermum gelatinosum (Rhodophyta)
<p>Data used for Shainker-Connelly et al. in biorxiv: https://www.biorxiv.org/content/10.1101/2024.09.20.614195v1</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.