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.
335
datasets available to search
ShareScore release 0.9.0
Dataset results
335 results for “Theoretical”
Data from: Discovery and information-theoretic characterization of transcription factor binding sites that act cooperatively
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein–DNA interactions at the sequence level is through position weight matrices (PWMs) that estimate the joint probability of a DNA binding site sequence by assuming positional independence within the DNA sequence. Here we construct conditional PWMs that depend on the motif signatures in the flanking DNA sequence, by conditioning known binding site loci on the presence or absence of additional binding sites in the flanking sequence of each siteʼs locus. Pooling known sites with similar flanking sequence patterns allows for the estimation of the conditional distribution function over the binding site sequences. We apply our model to the Dorsal transcription factor binding sites active in patterning the Dorsal–Ventral axis of Drosophila development. We find that those binding sites that cooperate with nearby Twist sites on average contain about 0.5 bits of information about the presence of Twist transcription factor binding sites in the flanking sequence. We also find that Dorsal binding site detectors conditioned on flanking sequence information make better predictions about what is a Dorsal site relative to background DNA than detection without information about flanking sequence features.
Data from: Combined effects of natural enemies and competition for resources on a forest defoliator: a theoretical and empirical analysis
Explanations for the dynamics of insect outbreaks often focus on natural enemies, on the grounds that parasitoid and pathogen attack rates are high during outbreaks. While natural enemy models can successfully reproduce outbreak cycles, experiments have repeatedly demonstrated the importance of resource quality and abundance. Experiments, however, are rarely invoked in modeling studies. Here we combine mechanistic models, observational data, and field experiments to quantify the roles of parasitoid attacks and resource competition on the jack pine budworm, Choristoneura pinus. By fitting models to a combination of observational and experimental data, we show that parasitoid attacks are the main source of larval budworm mortality at low and intermediate budworm densities, but that resource competition is the main source of mortality at high densities. Our results further show that the effects of resource competition become more severe with increasing host tree age, and that the effects of parasitoids are moderated by strong competition between parasitoids for hosts. Allowing for these effects in a model of insect outbreaks leads to realistic outbreak cycles, while a host-parasitoid model without resource competition produces an unrealistic stable equilibrium. The effects of resource competition are modulated by tree age, which in turn depends on fire regimes. Our model therefore suggests that increases in fire frequency due to climate change may interact in complex ways with budworm outbreaks. Our work shows that resource competition can be as important as natural enemies in modulating insect outbreaks, while demonstrating the usefulness of high-performance computing in experimental field ecology.
Data from: Strong evidence of an Information-Theoretical Conservation Principle linking all discrete systems
<p>Diverse discrete systems share common global properties that lack a unifying theoretical explanation. However, constraining the simplest measure of total information (Hartley-Shannon) in a statistical mechanics framework reveals a principle, the Conservation of Hartley-Shannon Information (CoHSI) that directly predicts both known and unsuspected common properties of discrete systems, as borne out in the diverse systems of computer software, proteins and music. Discrete systems fall into two categories distinguished by their structure: heterogeneous systems in which there is a distinguishable order of assembly of the system's components from an alphabet of unique tokens (e.g. proteins assembled from an alphabet of amino acids), and homogeneous systems in which unique tokens are simply binned, counted and rank ordered. Heterogeneous systems are characterized by an implicit distribution of component lengths, with sharp unimodal peak (containing the majority of components) and a power-law tail, whereas homogeneous systems reduce naturally to Zipf's Law but with a drooping tail in the distribution. We also confirm predictions that very long components are inevitable for heterogeneous systems; that discrete systems can exhibit simultaneously both heterogeneous and homogeneous behavior; and that in systems with more than one consistent token alphabet (e.g. digital music), the alphabets themselves show a power-law relationship.</p>
An effective mutualism? The role of theoretical studies in ecology and evolution
<p>Theoretical models often have fundamentally different goals than do empirical studies of the same topic. Models can test the logic of existing hypotheses, explore the plausibility of new hypotheses, provide expectations that can be tested with data, and address aspects of topics that are currently inaccessible empirically. Theoretical models are common in ecology and evolution, and are generally well-cited, but I show that many citations appearing in non-theoretical studies are general to topic and a substantial proportion are incorrect. One potential cause of this pattern is that some functions of models are rather abstract, leading to miscommunication between theoreticians and empiricists. Such misunderstandings are often triggered by simplifying, logistical assumptions that modelers make. The 2018 Vice Presidential Symposium of the American Society of Naturalists included a variety of mathematical models in ecology and evolution from across several topics. Common threads that appear in the use of the models are identified, highlighting the power of a theoretical approach and the role of the assumptions that such models make.</p>
Data file for the paper "General Models for the Electrochemical Hydrogen Oxidation and Hydrogen Evolution Reactions – Theoretical Derivation and Experimental Results Under Near Mass-Transport Free Conditions", J. Phys Chem. C., 2016, DOI:10.1021/acs.jpcc.6b00011
<p>The data in this folder is supplementary information for the paper:<br /> Anthony Kucernak and Christopher Zalitis, "General Models for the Electrochemical Hydrogen Oxidation and Hydrogen Evolution Reactions – Theoretical Derivation and Experimental Results Under Near Mass-Transport Free Conditions", J. Phys Chem. C., 2016, DOI:10.1021/acs.jpcc.6b00011</p> <p>The information is © Anthony Kucernak</p> <p>A description of the models used in these files is provided in that paper. Below is a description of the files</p> <p>Experimental Data.xlsx - This file contains the experimental data used to produce figures 6 and 7 in the aforementioned paper<br /> Model.xlsx - This file contains verified versions of the Heyrovsky-Volmer, Tafel-Volmer and Heyrovsky-Tafel-Volmer mechanisms developed in the paper mentioned above. These excel spreadsheets may be used to fit experimental data user the Solver function in Excel.</p> <p>Heyrovsky-Tafel.cdf, Heyrovsky-Tafel-Volmer.cdf, Tafel-Volmer.cdf, Heyrovsky-Volmer.cdf - These are "computable document format" files produced using Wolfram Mathematica. They allow easy and quick modification of model parameters to allow real-time exploration of the effect of the parameters on current density (as linear and Tafel plots), hydrogen coverage, Effective Tafel slope, and derived parameters. The CDF viewer is availble to download from the Wolfram site - www.wolfram.com</p>
FIGURE 2. A in The Scolopendra species (Chilopoda: Scolopendromorpha: Scolopendridae) of Greece (E-Mediterranean): a theoretical approach on the effect of geography and palaeogeography on their distribution
FIGURE 2. A) The distribution of species of the canidens group in Greece according to Zapparoli (2002). Black circles: S. clavipes, asterisks: S. cretica, black triangles: S. dalmatica, black arrows: S. canidens (the southern black arrow indicates an uncertain data from Gavdos Is.), B) The distribution of Scolopendra cingulata in Greece according to Zapparoli (2002). Black arrows indicate data from the Aegean Islands whereas black circles indicate data from mainland Greece and Ionian Islands.
FIGURE 4 in The Scolopendra species (Chilopoda: Scolopendromorpha: Scolopendridae) of Greece (E-Mediterranean): a theoretical approach on the effect of geography and palaeogeography on their distribution
FIGURE 4. The palaeogeography of Greece from Miocene to present (redrawn after Creutzburg 1963; Dermitzakis and Papanikolaou 1981; Dermitzakis 1990 and recently published by Parmakelis et al. 2005 and Poulakakis et al. 2005b, 2005c). The maps are drawn based on present geography. Gray: land, white: sea, black: lakes.
FIGURE 3. A in The Scolopendra species (Chilopoda: Scolopendromorpha: Scolopendridae) of Greece (E-Mediterranean): a theoretical approach on the effect of geography and palaeogeography on their distribution
FIGURE 3. A) The distribution of species of the Scolopendra canidens group in the Aegean Archipelago based on new data and bibliographic references, B) The distribution of Scolopendra cingulata in the Aegean Archipelago based on new data and bibliographic references.
FIGURE 5 in The Scolopendra species (Chilopoda: Scolopendromorpha: Scolopendridae) of Greece (E-Mediterranean): a theoretical approach on the effect of geography and palaeogeography on their distribution
FIGURE 5. The proposed chronicle of dispersal of S. canidens, S. cretica and S. cingulata in Greece based on schematic views of the palaeogeographic evolution of the Mediterranean and the Paratethys regions during the Miocene (Roegl and Steininger 1983). A: Middle Miocene (16-14.5 Mya), B: Upper Miocene (12-9 Mya). 1: Mainland Greece, 2: Crete, 3: Turkey, 4: Mid-Aegean trench, 5: Disjunction of Crete from mainland Greece and Cyclades Plateau, Scn: Scolopendra canidens, Sci: Scolopendra cingulata, Scr: Scolopendra cretica. Black: evaporitic sea areas, white: land areas, wavelike: sea areas, chesslike: low salinity sea areas.
Mechanistic insight into palladium-catalyzed cycloisomerization: A combined experimental and theoretical study
<p>Gaussian09 output files for all TPSS/def2-TZVP optimised stationary points from the above article.</p>
Data for "Solving the OH + glyoxal problem: A complete theoretical description of post transition state energy deposition in activated systems."
Open the record for dataset details and reuse information.
Enhanced perfusion following exposure to radiotherapy: a theoretical investigation (revised manuscript data)
<p>Dataset and software supporting the revised manuscript: "Enhanced perfusion following exposure to radiotherapy: a theoretical investigation." See the enclosed README and manuscript for further information.</p>
Experimental and theoretical analysis of ultrafast electron diffraction (UED) data for acetylacetone
<p>Here, in two archives with data for ultrafast electron diffraction (UED) study of the acetylacetone.</p><ol><li><a href="https://zenodo.org/api/records/10206479/draft/files/AcAc_UED_theoretical.zip/content">AcAc_UED_theoretical.zip</a> contains the results of theoretical simulations.</li><li><a href="https://zenodo.org/api/records/10206479/draft/files/AcAc_UED_experimental.zip/content">AcAc_UED_experimental.zip</a> contains raw and processed experimental data and scripts for data processing.</li></ol><p>Within each of the ZIP archives, the README files provide information on the actual data content within. </p>
Data and geometries for "Theoretical Investigation of Transient Species following Photodissociation of Ironpentacarbonyl in Ethanol Solution"
<p>Geometries and raw data for the paper "Theoretical Investigation of Transient Species following Photodissociation of Ironpentacarbonyl in Ethanol Solution"</p> <p>This work has received funding from the Swedish Research Council (grant agreement no. 2021-04521 and no. 2019-04796) and from Carl Tryggers Foundation (contract CTS18:285). The computations were enabled by resources provided by the National Academic Infrastructure for Supercomputing in Sweden (NAISS) and the Swedish National Infrastructure for Computing (SNIC) at NSC and PDC partially funded by the Swedish Research Council through grant agreements no. 2022-06725 and no. 2018-05973.</p> <p>Example inputs for the quantum chemistry optimizations.</p> <p>QUANTUM-CHEMISTRY/PDOS/GAS contains an example input of a projected density of states (PDOS) calculation of the TPSSh/def2-TZVP + CPCM(ethanol) optimized structure of Fe(CO)5.</p> <p>QUANTUM-CHEMISTRY/PDOS/LIQUID contains an example input of a projected density of states (PDOS) calculation for the time t = 0 fs configuration in the AIMD simulation of Fe(CO)5 in ethanol.</p> <p>QUANTUM-CHEMISTRY/DLPNO-CCSD contains an example input of a DLPNO-CCSD(T) energy calculation of the TPSSh/def2-TZVP + CPCM(ethanol) optimized structure of Fe(CO)5.</p> <p>QUANTUM-CHEMISTRY/TPSSh-OPTIMIZATION contains an example optimization and transition state optimization of Fe(CO)5 and Fe(CO)4-OH AX to EQ at the TPSSh/def2-TZVP + CPCM(ethanol) level of theory.</p> <p>QUANTUM-CHEMISTRY/TPSSh-OPTIMIZATION/MINIMA contains all of the TPSSh/def2-TZVP + CPCM(ethanol) optimized minima summarized in Table 1 in the main paper.</p> <p>QUANTUM-CHEMISTRY/TPSSh-OPTIMIZATION/TS-STRUCTURES contains all of the TPSSh/def2-TZVP + CPCM(ethanol) optimized transition state structures summarized in Table 1 in the main paper.</p> <p><br>Example inputs and outputs for the AIMD simulations which are necessary to reproduce the figures. In AIMD the following names correspond to the following simulations:</p> <p>Fe(CO)5 in the singlet state<br>FeCO5EtOH100</p> <p>Fe(CO)4 in the singlet state coordinated to an ethanol via the -OH group<br>FeCO4S1EtOH100</p> <p>Fe(CO)4 in the triplet state<br>FeCO4T1EtOH100</p> <p>Fe(CO)4 in the singlet state coordinated to an ethanol via the -HC group on the alpha carbon<br>FeCO4EtOHS1EtOH99</p> <p>Fe(CO)4 in the singlet state coordinated to an ethanol via the -HC group on the beta carbon<br>FeCO4EtOHBS1EtOH99</p>
Theoretical simulations for: Emergence of exotic spin texture in supramolecular metal complexes on a 2D superconductor
<p>Here you will find the information necessary to reproduce the theoretical data published on "Emergence of Exotic Spin Texture in Supramolecular Metal Complexes on a 2D Superconductor" paper</p> <p>It contains:</p> <ol> <li>the geometries used in the DFT calculations</li> <li>inputs and outputs of the multiplet calculations implemented on matlab</li> </ol>
Theoretical insights into the antiradical activity and copper-catalyzed oxidative damage of mexidol in the physiological environment
<p>This dataset contains data from the calculations described in the paper: "Quan V. Vo*, Nguyen Thi Hoa, <span class="fontstyle01"><span>Mai Van Bay, </span></span>Adam Mechler, Theoretical insights into the antiradical activity and copper-catalyzed oxidative damage of mexidol in the physiological environment. Royal Society Open Science. 2021.</p> <p>In this study, the hydroperoxyl radical scavenging activity of<b> MD </b>was studied to establish baseline antioxidant activity, followed by an investigation of the effect of<b> MD </b>on the <span class="fontstyle01"><span>copper-catalyzed oxidative damage in</span></span> <span class="fontstyle01"><span>biological systems, using computational methods. It was found that</span></span><span class="fontstyle01"><span><b> MD </b></span></span><span class="fontstyle01"><span>exhibits moderate </span></span>radical scavenging activity against HOO<sup>·</sup> in physiological environments. The activity in aqueous solution is defined by the single electron transfer mechanism of the anion state; however in nonpolar environments the formal hydrogen transfer pathway dominates at the O3-H bond. It was also confirmed that<b> MD </b><span class="fontstyle01"><span>can chelate Cu (II), forming complexes that are much harder to reduce than free Cu (II):</span></span><span class="fontstyle01"><span><b> MD </b></span></span><span class="fontstyle01"><span>chelation completely quenches the Cu (II) reduction by ascorbic acid and suppresses the rate of reduction reaction by O<sub>2</sub></span></span><span class="fontstyle01"><span><sup>·</sup></span></span><span class="fontstyle01"><span><sup>-</sup></span></span><span class="fontstyle01"><span> that are the main reductants of Cu (II) in biological environments. Therefore,</span></span><span class="fontstyle01"><span><b> MD </b></span></span><span class="fontstyle01"><span>exerts its anti- HO</span></span><span class="fontstyle01"><span><sup>·</sup></span></span><span class="fontstyle01"><span><sup> </sup></span></span><span class="fontstyle01"><span>activity primarily as an OIL-1 inhibitor. </span></span></p>
Figure 1 in A theoretical composite model for population sex-specific shell size dynamics in Strombidae (Gastropoda, Neostromboidae)
Figure 1. Modelling male and females population distribution curves showing the mean size (μ) of each sex and the (1) Sex dependant factors: a) time to maturity; b) intra-male competition; c) femalespecific sexual selection; d) fecundity; (2) Inter-sex dependant factors: e) time to maturity; f) sex bias towards larger numbers of females; and (3) Population factors: g) environmental conditions; and h) universal size regulators that affect the size ratio between females and males.
Theoretical investigations on shadow band correction factors for diffuse radiation under isotropic conditions without approximation dataset
<p>The database consists of: </p> <p>1. The data for the correction factors C<sub>h</sub> and C<sub>e </sub> (<strong>Data file for factors Ch and Ce</strong>);</p> <p>2. The data for figures 20, 21 and 22 (<strong>Data file for Figure 20, 21 and 22</strong>) ;</p> <p>3. The data for figure 23 (<strong>Data file for Figure 23</strong>) ;</p> <p>4. The data for figure 24 (<strong>Data file for Figure 24</strong>) ;</p> <p>5. The data for figure 25 (<strong>Data file for Figure 26</strong>) ;</p> <p>6. The data for figure 26 (<strong>Data file for Figure 26</strong>);</p> <p>7. The data for figure 27 (<strong>Data file for Figure 27</strong>) ;</p> <p>8. The data for figure 28 (<strong>Data file for Figure 28</strong>) ;</p> <p>9. The data for the correction factors C<sub>h</sub>, C<sub>e</sub> and C<sub>B</sub> (<strong>Data file of comparison with Burek</strong>) ;</p> <p>10. The data for the correction factors C<sub>h</sub>, C<sub>e</sub> and C<sub>D</sub> (<strong>Data file of comparison with Drummond</strong>);</p> <p>11. Reference 7 (<strong>Michael J. Brooks and Lance W. Roberts (2016)</strong>)</p>
Theoretical Design of Optimal Molecular Qudits for Quantum Error Correction. Open data set
<p>Data supporting the original figures 1, 2, 3 and 4 of the related publication.</p>
Data of Publication "Theoretical rheo-physics of silk: Intermolecular associations reduce the critical specific work for flow-induced crystallization"
<p>Data of Publication:</p> <p><em>Theoretical rheo-physics of silk: Intermolecular associations reduce the critical specific work for flow-induced crystallization<br> Charley Schaefer and Tom C. B. McLeish<br> Citation: Journal of Rheology 66, 515 (2022); doi: 10.1122/8.0000411<br> View online: https://doi.org/10.1122/8.0000411</em></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.