cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18035391
title: [Data & Code] Turning Citation Networks Inside Out: Studying Science Using Content-Based Knowledge Graphs from LLM-Derived Taxonomies

description: Title:Turning Citation Networks Inside Out: Studying Science Using Content-Based Knowledge Graphs from LLM-Derived TaxonomiesAbstract:Scientific fields are usually studied using citations and other metadata, even though papers primarily transmit knowledge through their content. We present an “inside-out” approach that reconstructs a field structure directly from textual content by converting each paper into a small set of interpretable knowledge components. Using a large language model to induce domain-specific taxonomies and to label papers, we represent every publication as a triplet of measure, data type, and research-question type, and build a knowledge graph whose edges are weighted by shared papers. On a tightly curated corpus of 617 studies of intergenerational wealth mobility, this content-level graph reveals a stable methodological backbone—regression-based mobility measures, alongside substantial temporal variation in how dominant components are recombined into pairs and triads. Beyond frequency, we introduce normalized betweenness-to-connectivity ratios that highlight components and pairings that act as disproportionately important structural bridges relative to their prevalence, pointing to combinations that are central to the knowledge network despite limited uptake. Our work demonstrates how content-derived, taxonomy-driven graphs can complement citation-based science mapping by exposing the evolving architecture of methods, data, and questions that define a research field.Data List:



LLM_prompts_summary.py: All the prompts used to generate and assign taxonomy categories.

figures.ipynb: To reproduce the figures in the paper with this notebook

edge_capa_investigation.ipynb: To investigate the changes in edge capacitance with an additional triplet into the network. (Note that other types of investigations are possible, as functions are added in edge_capacitance_inquiry.py)

random_graph.ipynb: To create random graphs. 

fig_network_graphml_lightcolor.gexf: Gephi file for visualization of the network


 

More can be found in our GitHub repository.
DOI: 10.5281/zenodo.15319844
title: Ultrafast heat transfer in single palladium nanocrystals seen with an X-ray free-electron laser

description: Here we present the processed coherent X-ray diffraction patterns and data analysis scripts for the paper titled "Ultrafast heat transfer in single palladium nanocrystals seen with an X-ray free-electron laser" published in Communications Materials (2026). Please see the README file for more information.
DOI: 10.5281/zenodo.15319843
title: Ultrafast heat transfer in single palladium nanocrystals seen with an X-ray free-electron laser

description: Here we present the processed coherent X-ray diffraction patterns and data analysis scripts for the paper titled "Ultrafast heat transfer in single palladium nanocrystals seen with an X-ray free-electron laser" published in Communications Materials (2026). Please see the README file for more information.
DOI: 10.15468/dl.r4kxqf
title: Occurrence Download

description: A dataset containing 29919 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Antarctica",
 "OccurrenceStatus is Present",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 29919 records from 188 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012468-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25824/redu/vzwkwd
title: Conceptual model of geomechanical facies in the Barra Velha Formation, northeastern Búzios Field, Brazil

description: Orthographic view of the 3D conceptual model depicting the spatial distribution of geomechanical facies within the Barra Velha Formation in the northeastern sector of the Búzios Field. The model, displayed with a 5× vertical exaggeration, highlights the relationship between GMFs and carbonate rock types (grain-size variability and evidence of subaerial exposure), as well as the main structural domains comprising shallow, slope, and bottom settings. The variation in Unconfined Compressive Strength (UCS) across the facies is indicated, illustrating its correlation with lake depth.
DOI: 10.6073/pasta/8d4fdbf2917c632028f92072f548a67f
title: Physarum polycephalum Repeated Maze Honors Thesis, Tulane University, SE Louisiana 2024-2025

description: We conducted an experimental maze study from January to March, 2025, on Physarum polycephalum at Tulane University in New Orleans, Louisiana. We collected data on changes in locomotive behavior as P. polycephalum repeatedly solved the same maze. From daily photographs of growth, we recorded path choice, contamination presence and location, number of times P. polycephalum grew directly over maze walls, how many of the four dead-ends P. polycephlaum grew down, and efficiency through surface area covered. Data collection is complete. We found a significant increase in efficiency, and a significant decrease in both dead-end paths and wall jumping, as maze repetitions increased. This points to evidence of information storage and retrieval, and therefore cognitive processes such as memory, within the single-cellular protist Physarum polycephalum.
DOI: 10.5281/zenodo.18261453
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS260115s Initial

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS260115s Initial. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.13012/b2idb-3414707_v1
title: Data for "Adsorptive Separation and Recovery of Triacetic Acid Lactone from Fermentation Broth"

description: Triacetic acid lactone (TAL) can be microbially produced and further chemically upgraded to several high-value chemicals. In this work, several acidic and basic ion-exchange resins and activated charcoal were evaluated for their ability to adsorb microbially produced TAL. Activated charcoal and a weak base resin, Dowex 66, showed similar TAL adsorption capacity of 0.18 ± 0.002 g/g. At 15% w/v activated charcoal, about 98% of TAL present in fermentation broth could be adsorbed. Further, ethanol washing allowed recovery of 72% of adsorbed TAL. A biorefinery producing TAL from sucrose was designed, simulated, and evaluated (through technoeconomic analysis) under uncertainty, for an estimated TAL minimum product selling price (MPSP) of $4.27/kg [$3.71−4.94/kg; 5th-95th percentiles] for the current state of technology and $2.83/kg [$2.46–3.29/kg] following potential near-term improvements to fermentation. Thus, this work provides an adsorptive process to recover microbially produced TAL that can be chemically upgraded to several industrial products.
DOI: 10.5281/zenodo.18261454
title: Submitted Galaxy Scores to the Gravitational Wave Treasure Map for event MS260115s Initial

description: Attached in a .json file is the ranked galaxy information within the contour region of the EM counterpart search associated with the gravitational wave event MS260115s Initial. A reference to these calculations can be found here: https://ui.adsabs.harvard.edu/abs/2017ApJ...848L..33A/abstract
DOI: 10.17909/r2dr-mq75
title: Data from paper, "A spectroscopically confirmed, strongly lensed, metal-poor Type II supernova at z = 5.13"

description: All HST and JWST observations used in the article: "A spectroscopically confirmed, strongly lensed, metal-poor Type II supernova at z = 5.13". Both HST data from 2012 showing a non-detection for the titular supernova as well as 2024 data showing a FUV detection are included. JWST data from the initial detection epoch and follow-up DDT program are further included.
DOI: 10.15468/dl.4m4xr2
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cicer subaphyllum"
 ]
}

 The dataset includes 13 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012471-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18200679
title: Heat stress affects taxonomic composition but not functional structure of reef fish assemblage in a thermal transition zone in the Southwestern Atlantic
DOI: 10.5281/zenodo.18200680
title: Heat stress affects taxonomic composition but not functional structure of reef fish assemblage in a thermal transition zone in the Southwestern Atlantic
DOI: 10.15468/dl.h76rhy
title: Occurrence Download

description: A dataset containing 13930 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Ochotona princeps)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 13930 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012472-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/vn2w-wv57
title: DIANA10 pollen surface sample dataset

description: Raw data for the DIANA10 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.acfzgp
title: Occurrence Download

description: A dataset containing 50265 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Scardinius erythrophthalmus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2010",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 50265 records from 163 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012460-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21233/0d42-gg15
title: CHISM2 pollen surface sample dataset

description: Raw data for the CHISM2 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.21233/4v76-4e71
title: ALTASUR4 pollen surface sample dataset

description: Raw data for the ALTASUR4 pollen surface sample dataset submitted to the Neotoma Paleoecology Database. Data is available through the landing page in JSON format. The landing page referenced by the DOI also contains links to publications and a map-based viewer for the dataset. The Neotoma Paleoecology Database maintains a homepage at https://www.neotomadb.org.
DOI: 10.15468/dl.vc4qkd
title: Occurrence Download

description: A dataset containing 3814339 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "Geometry POLYGON((-99.99096 15.50117,-94.43697 15.50117,-94.43697 18.46502,-99.99096 18.46502,-99.99096 15.50117))"
 ]
}

 The dataset includes 3814339 records from 1453 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012444-260108223611665/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nnudq5
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Arundo donax L., Carpobrotus acinaciformis (L.) L.Bolus, Carpobrotus edulis (L.) N.E.Br.)",
 "HasCoordinate is true",
 "Geometry POLYGON ((-8.739756 41.31534, -8.734044 41.3156, -8.731715 41.31591, -8.731583 41.31714, -8.731583 41.31749, -8.730617 41.31947, -8.730617 41.32272, -8.726223 41.32026, -8.72429 41.32035, -8.725388 41.32839, -8.72798 41.32835, -8.728639 41.32993, -8.730968 41.33041, -8.739888 41.32914, -8.739756 41.31534))"
 ]
}

 The dataset includes 43 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011601-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/r4t3vv372f
title: B Catenin is a downstream mediator of Pten and glycolysis

description: Uncropped western blot data published in the article entitled: "Glycolytic flux controls retinal progenitor cell differentiation via regulating Wnt signaling".
DOI: 10.17632/r4t3vv372f.1
title: B Catenin is a downstream mediator of Pten and glycolysis

description: Uncropped western blot data published in the article entitled: "Glycolytic flux controls retinal progenitor cell differentiation via regulating Wnt signaling".
DOI: 10.15468/dl.3wpp6s
title: Occurrence Download

description: A dataset containing 4173 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is France",
 "OccurrenceStatus is Present",
 "TaxonKey is Vipera ursinii (Bonaparte, 1835)"
 ]
}

 The dataset includes 4173 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002754-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5284/1129463
title: Images and a Vector Graphic from an Archaeological Watching Brief at Decoy House Farm, Watton, East Riding of Yorkshire, September 2020

description: This collection consists of images and a vector graphic from an archaeological watching brief by Headland Archaeology (UK) Ltd. Work occurred on land adjacent to Decoy House Farm, Watton, East Riding of Yorkshire in September 2020. A single ditch was excavated which was interpreted as associated with known cropmarks of a trackway.
DOI: 10.15468/dl.d7pth9
title: Occurrence Download

description: A dataset containing 12499 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Ambystoma opacum (Gravenhorst, 1807))"
 ]
}

 The dataset includes 12499 records from 47 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002757-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.akxjge
title: Occurrence Download

description: A dataset containing 36448 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Streptomyces Waksman & Henrici, 1943"
 ]
}

 The dataset includes 36448 records from 425 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014807-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14918097
title: Analysis of electron spectra dynamics in a moving periodical ponderomotive potential

description: Data for "Analysis of electron spectra dynamics in a moving periodical ponderomotive potential"
DOI: 10.5281/zenodo.14918098
title: Analysis of electron spectra dynamics in a moving periodical ponderomotive potential

description: Data for "Analysis of electron spectra dynamics in a moving periodical ponderomotive potential"
DOI: 10.5281/zenodo.15573422
title: Anomalous Magnetic Moments in Noncommutative Geometric Unification

description: This work establishes a universal mechanism for anomalous magnetic moments (AMM) within the noncommutative geometric unification framework. The quantum geometric fluctuations of the noncommutative parameter θµν generate AMM corrections for all fermions through the starcommutator term [θµν, γµγν]⋆. The effect scales as ∆a ∝ m2f /Λ^2NC with resonance enhancement at mf ∼ p⟨θ^2⟩. For the muon (mµ ≈ 105 MeV),we predict ∆aµ = (3.2 ± 1.1) × 10−9, resolving the current 4.2σ discrepancy. Electron AMM remains SM-compatible (∆ae < 10−13), while heavy fermions (τ , top quark) exhibit larger but experimentally challenging effects. The model is falsifiable through precision measurements at Fermilab, LHC, and next-generation storage rings.
DOI: 10.5281/zenodo.15573423
title: Anomalous Magnetic Moments in Noncommutative Geometric Unification

description: This work establishes a universal mechanism for anomalous magnetic moments (AMM) within the noncommutative geometric unification framework. The quantum geometric fluctuations of the noncommutative parameter θµν generate AMM corrections for all fermions through the starcommutator term [θµν, γµγν]⋆. The effect scales as ∆a ∝ m2f /Λ^2NC with resonance enhancement at mf ∼ p⟨θ^2⟩. For the muon (mµ ≈ 105 MeV),we predict ∆aµ = (3.2 ± 1.1) × 10−9, resolving the current 4.2σ discrepancy. Electron AMM remains SM-compatible (∆ae < 10−13), while heavy fermions (τ , top quark) exhibit larger but experimentally challenging effects. The model is falsifiable through precision measurements at Fermilab, LHC, and next-generation storage rings.
DOI: 10.15468/dl.gdh5e7
title: Occurrence Download

description: A dataset containing 2020 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Dicheirotrichus cognatus (Gyllenhal, 1827)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 2020 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0007427-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15190368
title: Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes

description: Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes

Supplementary publication data including:



Day 4, 9, and 15 GRNs in SBML format

Day 4, 9, and 15 Petri nets in SBML format

Day 4, 9, and 15 Petri net simulation results in CSV format

Day 15 small Petri net and miRNA knockout variant in SBML format

Day 15 small and miRNA knockout variant simulation results in CSV format

Rules file in YAML format for transforming GRNs to Petri nets in VANESA


Short manual of VANESA

Download:

VANESA is hostet on GitHub:https://github.com/cbrinkrolf/VANESAThe latest pre release (v.0.5_pre_2) is required.

Opening of networks:

Networks, biological networks and Petri nets, can be opened by "File" -> "Open File" (using the SBML file extension filter)

Opening transformation rules:

"Transformation" -> "Rule Management" -> "Load rules from file"Already available rules in VANESA should be removed first by clicking "Remove all rules". Rules can be set to active/inactive, viewed/edited, deleted, and their order can be manipulated.

Transforming a biological network to a Petri net:

If a biological network is loaded and transformation rules are also present, the biological network can be transformed to a Petri net by clicking: "Transformation" -> "Transform to Petri net".After successful transformation, the underlying Petri net can be shown by: "Transformation" -> "Show Petri net". This Petri net can be saved independently of the biological network it was generated from.

Run a Petri net simulation:

For the Petri net simulation, the installation of OpenModelica is required. Please install a compatible version of OpenModelica, such as OpenModelica 1.24.4.If a Petri net is loaded or generated, click "Petri Net" -> "Simulate" to show the simulation window. Set the stop time and, especially for larger networks, enable the developer options and select "use short model name" and "Eq. per file". Set the equations per file to 2000 before starting the simulation.

Saving and loading simulation results:

Computed simulation results shown in the simulation window can be set to active, renamed, exported as a CSV file, and deleted. Only active simulation results are shown in the "Petri Net Simulation" panel on the left side of the main window. If a Petri net is present, an already generated simulation result file can be loaded by clicking "Petri Net" -> "Load Simulation Result".

The simulation result(s) can be investigated by selecting one or multiple nodes or arcs.
DOI: 10.5281/zenodo.15190369
title: Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes

description: Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes

Supplementary publication data including:



Day 4, 9, and 15 GRNs in SBML format

Day 4, 9, and 15 Petri nets in SBML format

Day 4, 9, and 15 Petri net simulation results in CSV format

Day 15 small Petri net and miRNA knockout variant in SBML format

Day 15 small and miRNA knockout variant simulation results in CSV format

Rules file in YAML format for transforming GRNs to Petri nets in VANESA


Short manual of VANESA

Download:

VANESA is hostet on GitHub:https://github.com/cbrinkrolf/VANESAThe latest pre release (v.0.5_pre_2) is required.

Opening of networks:

Networks, biological networks and Petri nets, can be opened by "File" -> "Open File" (using the SBML file extension filter)

Opening transformation rules:

"Transformation" -> "Rule Management" -> "Load rules from file"Already available rules in VANESA should be removed first by clicking "Remove all rules". Rules can be set to active/inactive, viewed/edited, deleted, and their order can be manipulated.

Transforming a biological network to a Petri net:

If a biological network is loaded and transformation rules are also present, the biological network can be transformed to a Petri net by clicking: "Transformation" -> "Transform to Petri net".After successful transformation, the underlying Petri net can be shown by: "Transformation" -> "Show Petri net". This Petri net can be saved independently of the biological network it was generated from.

Run a Petri net simulation:

For the Petri net simulation, the installation of OpenModelica is required. Please install a compatible version of OpenModelica, such as OpenModelica 1.24.4.If a Petri net is loaded or generated, click "Petri Net" -> "Simulate" to show the simulation window. Set the stop time and, especially for larger networks, enable the developer options and select "use short model name" and "Eq. per file". Set the equations per file to 2000 before starting the simulation.

Saving and loading simulation results:

Computed simulation results shown in the simulation window can be set to active, renamed, exported as a CSV file, and deleted. Only active simulation results are shown in the "Petri Net Simulation" panel on the left side of the main window. If a Petri net is present, an already generated simulation result file can be loaded by clicking "Petri Net" -> "Load Simulation Result".

The simulation result(s) can be investigated by selecting one or multiple nodes or arcs.