cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15319453
title: Experimental Confirmation of the Interception History Paradigm for Colloid (Micro and Nanoparticle) Transport in Porous Media - Data

description: This dataset supports the findings presented in the manuscript “Experimental Confirmation of the Interception History Paradigm for Colloid Transport in Porous Media” by Johnson et al. (2025).

It includes both experimental and simulation data used to generate the figures and results reported in the study.

Contents:





Raw experimental data





AML: Favorable conditions




CML: Unfavorable conditions






Simulation data





Fav: Favorable conditions




Unfav: Unfavorable conditions




Includes both raw and filtered arrays






Processed data





Includes particle trajectories, velocities, and separation distance distributions






README file





Describes the folder structure, file naming conventions, and data organization





Scripts and Manual:

The MATLAB scripts used for data processing and figure generation, as well as a detailed user manual, are available on GitHub: luisullauri19/Johnsonetal2025: Experimental Confirmation of the Interception History Paradigm for Colloid (Micro and Nanoparticle) Transport in Porous Media - Code
DOI: 10.5281/zenodo.15319454
title: Experimental Confirmation of the Interception History Paradigm for Colloid (Micro and Nanoparticle) Transport in Porous Media - Data

description: This dataset supports the findings presented in the manuscript “Experimental Confirmation of the Interception History Paradigm for Colloid Transport in Porous Media” by Johnson et al. (2025).

It includes both experimental and simulation data used to generate the figures and results reported in the study.

Contents:





Raw experimental data





AML: Favorable conditions




CML: Unfavorable conditions






Simulation data





Fav: Favorable conditions




Unfav: Unfavorable conditions




Includes both raw and filtered arrays






Processed data





Includes particle trajectories, velocities, and separation distance distributions






README file





Describes the folder structure, file naming conventions, and data organization





Scripts and Manual:

The MATLAB scripts used for data processing and figure generation, as well as a detailed user manual, are available on GitHub: luisullauri19/Johnsonetal2025: Experimental Confirmation of the Interception History Paradigm for Colloid (Micro and Nanoparticle) Transport in Porous Media - Code
DOI: 10.6084/m9.figshare.28924526
title: Wendt & Nandke et al. 2025 gcb R code.txt

description: R code for creating a PCA, a backward selected multiple linear regression model, a correlation plot and and mlvr with predefined coefficients
DOI: 10.15482/usda.adc/25594929
title: Data from: New Record of the Pavement Ant, <i>Tetramorium immigrans</i> (Hymenoptera: Formicidae), in South Dakota with notes on its thermal tolerance and geographic distribution

description: Data files for manuscript titled "New Record of the Pavement Ant, <i>Tetramorium immigrans</i> (Hymenoptera: Formicidae), in South Dakota with Notes on its Thermal Tolerance and Geographic Distribution".Excel file with 7 tabs: Metadata; CTmin, CTmax, Knock-down, Chill coma, Specimen data, Observation dataData description: Raw data for county observations/museum collections and thermal traits of <i>Tetramorium immigrans</i>. The data for observations/museum collections were collated from &gt;100 years of publicly available information on the Global Biodiversity Information Facility (GBIF) and the Symbiota Collections of Arthropods Network (SCAN). Presence/absence values from these digital repositories were assigned to current county or county equivalent federal information processing system (FIPS) codes to create an updated distributional map. Thermal trait data that included critical thermal maximum and minimum, knock-down resistance, and chill coma recovery were empirically determined from specimens collected in Brookings, SD in 2022 and 2023. Methods for each assay are listed in the main text.Abstract from paper: The pavement ant, <i>Tetramorium immigrans</i> Santschi, is an abundant and widespread species across large portions of the United States. Yet despite its current distribution in Northeastern, Midwestern, Pacific, and Western states, there is a surprising lack of records from the Great Plains. Here we present an updated county list of <i>T. immigrans</i> from museum collections and research grade observations (459 counties; ~15% of US counties), highlighting the first records from one Great Plains state—South Dakota. Observations on community science platforms since 2006 have undoubtedly increased the awareness of <i>T. immigrans</i> (+329 counties; ~72% of all county records), however we posit that such platforms may also highlight the dispersal limitations of this species into the less urban, colder Northern Great Plains states of Montana, Nebraska, North Dakota, South Dakota, and Wyoming (~5% of 291 counties). As such, we offer novel information on <i>T. immigrans</i>’ thermal biology including measurements of critical thermal limits, knock-down resistance, and chill coma recovery. While <i>T. immigrans</i> can likely tolerate the warm summer temperatures found in South Dakota due to its heat tolerance hovering around 46 °C, its lower ability to tolerate cold winter conditions may be a possible mechanism for its limited dispersal.
DOI: 10.15482/usda.adc/25594929.v1
title: Data from: New Record of the Pavement Ant, <i>Tetramorium immigrans</i> (Hymenoptera: Formicidae), in South Dakota with notes on its thermal tolerance and geographic distribution

description: Data files for manuscript titled "New Record of the Pavement Ant, <i>Tetramorium immigrans</i> (Hymenoptera: Formicidae), in South Dakota with Notes on its Thermal Tolerance and Geographic Distribution".Excel file with 7 tabs: Metadata; CTmin, CTmax, Knock-down, Chill coma, Specimen data, Observation dataData description: Raw data for county observations/museum collections and thermal traits of <i>Tetramorium immigrans</i>. The data for observations/museum collections were collated from &gt;100 years of publicly available information on the Global Biodiversity Information Facility (GBIF) and the Symbiota Collections of Arthropods Network (SCAN). Presence/absence values from these digital repositories were assigned to current county or county equivalent federal information processing system (FIPS) codes to create an updated distributional map. Thermal trait data that included critical thermal maximum and minimum, knock-down resistance, and chill coma recovery were empirically determined from specimens collected in Brookings, SD in 2022 and 2023. Methods for each assay are listed in the main text.Abstract from paper: The pavement ant, <i>Tetramorium immigrans</i> Santschi, is an abundant and widespread species across large portions of the United States. Yet despite its current distribution in Northeastern, Midwestern, Pacific, and Western states, there is a surprising lack of records from the Great Plains. Here we present an updated county list of <i>T. immigrans</i> from museum collections and research grade observations (459 counties; ~15% of US counties), highlighting the first records from one Great Plains state—South Dakota. Observations on community science platforms since 2006 have undoubtedly increased the awareness of <i>T. immigrans</i> (+329 counties; ~72% of all county records), however we posit that such platforms may also highlight the dispersal limitations of this species into the less urban, colder Northern Great Plains states of Montana, Nebraska, North Dakota, South Dakota, and Wyoming (~5% of 291 counties). As such, we offer novel information on <i>T. immigrans</i>’ thermal biology including measurements of critical thermal limits, knock-down resistance, and chill coma recovery. While <i>T. immigrans</i> can likely tolerate the warm summer temperatures found in South Dakota due to its heat tolerance hovering around 46 °C, its lower ability to tolerate cold winter conditions may be a possible mechanism for its limited dispersal.
DOI: 10.15468/dl.4f8ph4
title: Occurrence Download

description: A dataset containing 40005 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-114.75036 32.50613,-111.11117 31.29773,-108.22128 31.30529,-108.38377 38.08214,-114.75188 38.09636,-114.75036 32.50613))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "StateProvince is one of (Maricopa County, Arizona)",
 "TaxonKey is Mammalia",
 "Year 2013-2023"
 ]
}

 The dataset includes 40005 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012131-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y9te6u
title: Occurrence Download

description: A dataset containing 1068 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Machine Observation, Specimen)",
 "Country is Brazil",
 "DatasetKey is one of (iNaturalist Research-grade Observations, Global Roadkill Data: a dataset on terrestrial vertebrate mortality caused by collision with vehicles (Systematic Records), Brandt Meio Ambiente - Monitoramento da mastofauna terrestre - Usina Hidrelétrica de São Simão, Global Roadkill Data: a dataset on terrestrial vertebrate mortality caused by collision with vehicles (Opportunistic Records), NABU|naturgucker, Coleção de Mamíferos da Universidade Estadual de Goiás, Projeto Conexão Mata Atlântica - Monitoramento Ecossistêmico - Fauna e Flora - São Paulo - Campanha 05, Projeto Conexão Mata Atlântica - Monitoramento Ecossistêmico - Fauna e Flora - São Paulo - Campanha 06, MVZ Mammal Collection (Arctos), Projeto Conexão Mata Atlântica - Monitoramento Ecossistêmico - Fauna e Flora - São Paulo - Campanha 03)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Tapiridae",
 "Year is greater than or equal to 1990"
 ]
}

 The dataset includes 1068 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012132-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jx3wre
title: Occurrence Download

description: A dataset containing 2943503 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 Catharus guttatus (Pallas, 1811)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 2943503 records from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012127-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7s6gxs
title: Occurrence Download

description: A dataset containing 6040 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Pinguicula vulgaris L.",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 6040 records from 44 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012133-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3qhqh
title: Occurrence Download

description: A dataset containing 2847 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Jupunba trapezifolia var. micradenia (Benth.) M.V.B.Soares, M.P.Morim & Iganci"
 ]
}

 The dataset includes 2847 records from 200 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012134-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wpzha6
title: Occurrence Download

description: A dataset containing 1048 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Calathus micropterus (Duftschmid, 1812)",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1048 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012136-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qttxc7
title: Occurrence Download

description: A dataset containing 48553 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 {
 "or" : [
 "InstitutionKey is not null",
 "CollectionKey is not null"
 ]
 },
 "BasisOfRecord is one of (Specimen, Fossil, Material sample, Living Specimen, Material citation)"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Mammalia, Rodentia)",
 "Country is one of (Bolivia (Plurinational State of))"
 ]
 }
 ]
}

 The dataset includes 48553 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012135-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15785/sbgrid/1158
title: X-Ray Diffraction data from c-Src SH3 domain, source of 9OFX structure

description: X-Ray Diffraction data for c-Src SH3 domain
description: anomalous signal is present in data from ordered Ni ions
DOI: 10.15468/dl.ryd6t8
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gymnogyps californianus (Shaw, 1797)",
 "Year 2003-2003"
 ]
}

 The dataset includes 160 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012139-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17909/hqaf-an74
title: NIRCam observation for high-z QSO

description: NIRCam observation for SHELLQs 12 z>6 QSOs for studying the host galaxies.
DOI: 10.5281/zenodo.15330596
title: PharmaKG Explorer: Knowledge Graph Embedding-Driven Conversational Querying and Real Time Link Prediction in Drug-Gene-Disease Networks

description: In this project, we develop an end-to-end platform for interactive knowledge graph embedding tailored to accelerate drug discovery. Starting from curated biomedical datasets-PharmAlchemy, we extract and filter 311496 triplets linking drugs, genes, diseases, and side effects, then deploy the complete graph including nodes, relations, and properties on Neo4j Aura. A natural‑language interface built with Gradio and LangChain leverages LLM prompting (Gemma2‑9b‑It) to translate user inputs into Cypher queries, enabling seamless, conversational exploration of the graph. We also implemented and compared three state‑of‑the‑art embedding methods - TransE, RotatE, and ComplEx- on link prediction benchmarks, evaluating performance via metrics such as Hits@k and mean reciprocal rank. To make link prediction findings actionable, we also provide an interactive GUI that allows researchers to visualize and test potential new relationships in real time. This integrated framework combines powerful embedding techniques with user‑friendly interfaces to support rapid hypothesis generation and discovery in biomedical research.
DOI: 10.5281/zenodo.15330597
title: PharmaKG Explorer: Knowledge Graph Embedding-Driven Conversational Querying and Real Time Link Prediction in Drug-Gene-Disease Networks

description: In this project, we develop an end-to-end platform for interactive knowledge graph embedding tailored to accelerate drug discovery. Starting from curated biomedical datasets-PharmAlchemy, we extract and filter 311496 triplets linking drugs, genes, diseases, and side effects, then deploy the complete graph including nodes, relations, and properties on Neo4j Aura. A natural‑language interface built with Gradio and LangChain leverages LLM prompting (Gemma2‑9b‑It) to translate user inputs into Cypher queries, enabling seamless, conversational exploration of the graph. We also implemented and compared three state‑of‑the‑art embedding methods - TransE, RotatE, and ComplEx- on link prediction benchmarks, evaluating performance via metrics such as Hits@k and mean reciprocal rank. To make link prediction findings actionable, we also provide an interactive GUI that allows researchers to visualize and test potential new relationships in real time. This integrated framework combines powerful embedding techniques with user‑friendly interfaces to support rapid hypothesis generation and discovery in biomedical research.
DOI: 10.5281/zenodo.15330629
title: sessilanthera_heliantha_spades_01.fasta.gz
DOI: 10.5281/zenodo.15330630
title: sessilanthera_heliantha_spades_01.fasta.gz
DOI: 10.5281/zenodo.15321801
title: Data for: "Spin-correlated radical pair dynamics controlled by magnetic resonance in a transgenic animal"

description: Files Fig_2_data.zip and Fig_3_data.zip contain data (.csv format) for generating figures shown in Figs. 2 and 3 in the manuscript. Note that the datasets for panel 2A are numbered in decreasing order of RF amplitude.  




Fig_4_data.zip contains data relevant for Fig. 4 in two folders, Fig_4ABC and Fig_4DEF for the upper and lower panels of the figure respectively.  Each folder contains two .npy files with an array of images (as numpy arrays) over the course of the experiment, one with the original images, and one with the images divided into blocks for analysis as described in the manuscript text and SI.  The .npz files contain the RYDMR and MFE maps obtained from analysis of the blocked image sequence. The .csv files in Fig_4_data.zip contain example analysis results (similar to the data shown in Figs. 4 A and D) from camera counts integrated from within a circle with radius of 10 pixels (in the original images). The center coordinates of the circles are (221,76) for RYDMR_wrmSc.csv and (81,76) for RYDMR_wrmSc_control.csv. These may be very slightly shifted relative to the coordinates used for the data in the main text, but this does not result in significant changes to the results or interpretation.  The first column in each .csv file is the time (t) in seconds relative to the start of the B_0 scans. Corresponding B_0 values for two scans are given in column 2. The remaining columns contain the fluorescence data (normalized to the camera counts measured at t=0), the estimate bleaching function (see SI in the manuscript), the fluorescence with the bleaching function subtracted, and the final fit data used to estimate the MFE and RYDMR.
DOI: 10.5281/zenodo.15272788
title: scRNA-seq datasets used in scAGCL

description: This datasets is used in the study of scAGCL. The datasets are collected from other published studies (Datasets used in scMAE, 



https://github.com/xuebaliang/scziDesk,  GitHub - gushenweiz/scCAEs).
DOI: 10.5281/zenodo.15272789
title: scRNA-seq datasets used in scAGCL

description: This datasets is used in the study of scAGCL. The datasets are collected from other published studies (Datasets used in scMAE, 



https://github.com/xuebaliang/scziDesk,  GitHub - gushenweiz/scCAEs).
DOI: 10.15468/7ncfru
title: The flora and fauna at Ram and Mula river confluence, Baner-Aundh link road, Pune, India

description: The dataset consists of multi taxa species occurrences from a observational study carried out at the confluence zone of the Mula and Ram river, Baner, Pune. The survey included various riverine habitats including the channel, bed, bank, adjacent riparian forest and the streams that flow into the river.
DOI: 10.15468/dl.n9xyhn
title: Occurrence Download

description: A dataset containing 13299011 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 Melanerpes carolinus (Linnaeus, 1758)",
 "Year is greater than or equal to 1950",
 {
 "or" : [
 "GadmGid is USA",
 "GadmGid is CAN",
 "GadmGid is MEX"
 ]
 }
 ]
}

 The dataset includes 13299011 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012137-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vq6cww
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((154.75025 -5.39308,154.60187 -5.53733,154.73788 -6.61306,155.62814 -6.95514,155.99908 -6.84798,156.02381 -6.51002,155.35612 -5.67334,154.91923 -5.37659,154.75025 -5.39308))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Formicidae"
 ]
}

 The dataset includes 57 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012142-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4kb4hz
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "EventDate is less than or equal to 2000-02-01",
 "Geometry POLYGON((-73.91957 40.91972,-73.96557 40.82418,-74.01637 40.75972,-74.02667 40.70196,-74.05413 40.65197,-74.08915 40.64989,-74.09876 40.6478,-74.13789 40.64416,-74.16124 40.64728,-74.17772 40.64728,-74.19351 40.64364,-74.20312 40.62748,-74.20518 40.61185,-74.19969 40.59986,-74.20724 40.58891,-74.21479 40.55709,-74.23333 40.5597,-74.24569 40.5524,-74.25049 40.54248,-74.24775 40.52265,-74.25804 40.51169,-74.26148 40.49916,-74.25942 40.48872,-74.22509 40.47566,-73.97861 40.51952,-73.9024 40.49081,-73.89279 40.5049,-73.80422 40.53152,-73.76234 40.53257,-73.75891 40.56179,-73.73351 40.58526,-73.74586 40.60611,-73.76852 40.61497,-73.76989 40.62488,-73.75067 40.63061,-73.74106 40.64624,-73.72252 40.64885,-73.72939 40.66656,-73.71771 40.71446,-73.69849 40.7488,-73.75067 40.7826,-73.77882 40.81015,-73.78088 40.82574,-73.75754 40.84496,-73.74724 40.87197,-73.91957 40.91972))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Pseudacris crucifer (Wied-Neuwied, 1838)"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0012143-250426092105405/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.