cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17195043
title: Computational data for the degradation of BPA under Fenton-type conditions

description: This repository contains the most relevant data obtained at the different calculation levels described in the manuscript. The contents are briefly explained below.

1. AutoMeKin/: This directory contains the possible unimolecular reaction pathways of BPA degradation under Fenton-type conditions, obtained in AutoMeKin. Each subdirectory, identified by the name of the chemical species indicated in the article, contains:

    1.1.- *.dat file corresponding to the input of the species to be studied in AutoMeKin.

    1.2.- *.xyz file corresponding to the structure in cartesian coordinates of the species to be studied.

    1.3.- FINAL_LL* subdirectory containing the results of the "Low Level" calculations obtained using the semi-empirical PM7 method.

    1.4.- FINAL_HL* subdirectory containing the results of the "High Level" calculations obtained using the HF/3-21G method.

Detailed explanations about the installation and use of AutoMeKin can be found at:

    https://github.com/emartineznunez/AutoMeKin

2. DFT/: This directory contains the results of the ωB97XD/def2-TZVPP calculations for each of the chemical species explained in the article. The content is divided into three subdirectories:

    2.1. GAS/: This folder contains the Gaussian ".log" files for the chemical species. Each file is identified with the same name as the article. In the case of transition states, the acronyms accompanying "TS" correspond to the minimum generated by the respective TS. TSs that include "w1" and "w2" in their names correspond to calculations in which one and two water molecules were included, respectively.

    2.2. IRC/: This directory contains “.molden” files describing the intrinsic reaction path (IRC) associated to each TS in the GAS/ folder.

    2.3. SMD/: This folder contains the solvent (H2O) correction for each of the results contained in GAS/. 

3. PILGRIM/: This folder contains the input files for the execution with Pilgrim, as well as the corresponding output files.

Detailed explanations about the installation and use of Pilgrim can be found at:

    https://github.com/cathedralpkg/Pilgrim

4. SI.pdf: a .pdf file containing data of interest for each step (Gibbs free energies and thermal rate constants).
DOI: 10.15468/dl.pdz22r
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "DatasetKey is UCM Fossil Vertebrate Specimens (Arctos)",
 "OccurrenceStatus is Present",
 "TaxonKey is Palaechthonidae"
 ]
}

 The dataset includes 21 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015330-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15654453
title: Computational data for the degradation of BPA under Fenton-type conditions

description: This repository contains the most relevant data obtained at the different calculation levels described in the manuscript. The contents are briefly explained below.

1. AutoMeKin/: This directory contains the possible unimolecular reaction pathways of BPA degradation under Fenton-type conditions, obtained in AutoMeKin. Each subdirectory, identified by the name of the chemical species indicated in the article, contains:

    1.1.- *.dat file corresponding to the input of the species to be studied in AutoMeKin.

    1.2.- *.xyz file corresponding to the structure in cartesian coordinates of the species to be studied.

    1.3.- FINAL_LL* subdirectory containing the results of the "Low Level" calculations obtained using the semi-empirical PM7 method.

    1.4.- FINAL_HL* subdirectory containing the results of the "High Level" calculations obtained using the HF/3-21G method.

Detailed explanations about the installation and use of AutoMeKin can be found at:

    https://github.com/emartineznunez/AutoMeKin

2. DFT/: This directory contains the results of the ωB97XD/def2-TZVPP calculations for each of the chemical species explained in the article. The content is divided into three subdirectories:

    2.1. GAS/: This folder contains the Gaussian ".log" files for the chemical species. Each file is identified with the same name as the article. In the case of transition states, the acronyms accompanying "TS" correspond to the minimum generated by the respective TS. TSs that include "w1" and "w2" in their names correspond to calculations in which one and two water molecules were included, respectively.

    2.2. IRC/: This directory contains “.molden” files describing the intrinsic reaction path (IRC) associated to each TS in the GAS/ folder.

    2.3. SMD/: This folder contains the solvent (H2O) correction for each of the results contained in GAS/. 

3. PILGRIM/: This folder contains the input files for the execution with Pilgrim, as well as the corresponding output files.

Detailed explanations about the installation and use of Pilgrim can be found at:

    https://github.com/cathedralpkg/Pilgrim

4. SI.pdf: a .pdf file containing data of interest for each step (Gibbs free energies and thermal rate constants).
DOI: 10.15468/dl.xuukfz
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Cottus hispaniolensis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 14 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015331-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15004651
title: Structural and electronic properties of SnTe nano flakes and nanowires
DOI: 10.5281/zenodo.17199186
title: Structural and electronic properties of SnTe nano flakes and nanowires
DOI: 10.15468/dl.8u94k8
title: Occurrence Download

description: A dataset containing 59 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 one of (Gerbera jamesonii)"
 ]
}

 The dataset includes 59 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015333-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6btthy
title: Occurrence Download

description: A dataset containing 173 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Buxus wallichiana"
 ]
}

 The dataset includes 173 records from 25 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015332-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4pgb33
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea macrothyrsa",
 "Country is Czechia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015335-250920141307145/datasets/export for details.
DOI: 10.15468/dl.eq93wr
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea macrothyrsa",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015334-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17199206
title: Multifunctional tris(triazolo)triazine-based emitter with dual-TADF, RTP, AIEE and AIDF properties

description: This dataset is associated with the figures presented in the work with the same title. It also contains additional data to support the Experimental Section (e.g., NMR and HRMS).
DOI: 10.5281/zenodo.17199207
title: Multifunctional tris(triazolo)triazine-based emitter with dual-TADF, RTP, AIEE and AIDF properties

description: This dataset is associated with the figures presented in the work with the same title. It also contains additional data to support the Experimental Section (e.g., NMR and HRMS).
DOI: 10.15468/dl.fyrk99
title: Occurrence Download

description: A dataset containing 147 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea macrothyrsa",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 147 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015336-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jf82v3
title: Occurrence Download

description: A dataset listing the 1268 species recorded in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "Country is one of (Kenya, Uganda)",
 "DatasetKey is iNaturalist Research-grade Observations",
 "TaxonKey is Lepidoptera"
 ]
}

 The dataset's 1268 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015306-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.86p3r6
title: Occurrence Download

description: A dataset containing 4216 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Discoglossus galganoi)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 4216 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015338-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ugc4pc
title: Occurrence Download

description: A dataset containing 160 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material sample)",
 "TaxonKey is Cryptotis gracilis"
 ]
}

 The dataset includes 160 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015341-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rvjpxv
title: Occurrence Download

description: A dataset containing 189 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Specimen, Material sample)",
 "TaxonKey is Cryptotis merriami"
 ]
}

 The dataset includes 189 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015342-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17048562
title: A Handheld Tool for Temporal and Spatial Young's Modulus Characterization of Soft Materials: Towards Point-of-Care Soft Tissue Assessment (Experiment Data and Codes)

description: This repository contains the experiment codes, analysis codes, and data for the submission titled "A Handheld Tool for Temporal and Spatial Young's Modulus Characterization of Soft Materials: Toward Soft Tissue Assessment in Physical Examinations". The folder named "Final_Experiment_Codes_Zenodo" contains the experiment codes. The folder named "Final_Analysis_Codes" contains the analysis codes and experiment data. The "Final_Arduino_Code" folder contains the Arduino IDE code used for the SensoPal device.
DOI: 10.5281/zenodo.17048563
title: A Handheld Tool for Temporal and Spatial Young's Modulus Characterization of Soft Materials: Towards Point-of-Care Soft Tissue Assessment (Experiment Data and Codes)

description: This repository contains the experiment codes, analysis codes, and data for the submission titled "A Handheld Tool for Temporal and Spatial Young's Modulus Characterization of Soft Materials: Toward Soft Tissue Assessment in Physical Examinations". The folder named "Final_Experiment_Codes_Zenodo" contains the experiment codes. The folder named "Final_Analysis_Codes" contains the analysis codes and experiment data. The "Final_Arduino_Code" folder contains the Arduino IDE code used for the SensoPal device.
DOI: 10.15468/dl.y9dmsw
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "TaxonKey is Cryptotis monteverdensis"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015343-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15324016
title: Hayes2025_NAD-ciprofloxacin_mixtures

description: Data and Code for 'Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin'




DOI of the paper at ISME Communications: https://doi.org/10.1093/ismeco/ycaf169

Sequence data is deposited at ENA - Accession Number PRJEB88784.

All other data is deposited here as part of this repository and deposited on Zenodo




Outline


This repository contains the datasets and code, analysed as part of the study in the manuscript 'Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin'.

It contains the growth OD readings, qPCR assay gene quantities, and processed metagenome sequence data (directly from the AMR++ output). It also contains the code used to analyse these data and produce all figures in this paper. The code for running the bioinformatics pipelines are not present here, but can be run with default parameters. In this study we used AMR++ to analyse the metagenome data. AMR++ is well supported by a GitHub repository - https://github.com/Microbial-Ecology-Group/AMRplusplus.



Notes on the code


All code is written to be run in separate R projects. A project is associated with a group of folders, and all figures, scripts and data are kept within each folder. Personally, I keep my growth data in a folder called ‘Growth Analyses’, with a nested set of folders – data, figures, and scripts. An R project will be associated with these folders. Only the code and data are deposited here, but these can be altered to suit how you work best.
DOI: 10.5281/zenodo.17190299
title: Hayes2025_NAD-ciprofloxacin_mixtures

description: Data and Code for 'Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin'




DOI of the paper at ISME Communications: https://doi.org/10.1093/ismeco/ycaf169

Sequence data is deposited at ENA - Accession Number PRJEB88784.

All other data is deposited here as part of this repository and deposited on Zenodo




Outline


This repository contains the datasets and code, analysed as part of the study in the manuscript 'Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin'.

It contains the growth OD readings, qPCR assay gene quantities, and processed metagenome sequence data (directly from the AMR++ output). It also contains the code used to analyse these data and produce all figures in this paper. The code for running the bioinformatics pipelines are not present here, but can be run with default parameters. In this study we used AMR++ to analyse the metagenome data. AMR++ is well supported by a GitHub repository - https://github.com/Microbial-Ecology-Group/AMRplusplus.



Notes on the code


All code is written to be run in separate R projects. A project is associated with a group of folders, and all figures, scripts and data are kept within each folder. Personally, I keep my growth data in a folder called ‘Growth Analyses’, with a nested set of folders – data, figures, and scripts. An R project will be associated with these folders. Only the code and data are deposited here, but these can be altered to suit how you work best.
DOI: 10.15468/dl.ngs8am
title: Occurrence Download

description: A dataset containing 46564 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 one of (Calendula arvensis)"
 ]
}

 The dataset includes 46564 records from 634 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015344-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/55rk6g
title: Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Liu, Zhenwen, Liu, Ende, He, Deming, Ma, Yongpeng, Gao, Lianming (2023): Rhododendron mingii (Ericaceae), a new species from Southeast of Yunnan, China. Phytotaxa 619 (1): 97-104, DOI: 10.11646/phytotaxa.619.1.5, URL: http://dx.doi.org/10.11646/phytotaxa.619.1.5AbstractA new species of Rhododendron, R. mingii (Ericaceae), from Malipo County, Southeast of Yunnan, China is described and illustrated here. Morphologically, the new species is most similar to R. genestierianum but differs by its much shorter petiole and leaf, hairs along the margin of the leaf, densely white powder on outer surface of petal, and slender and erect style. A molecular phylogenetic analysis based on three standard DNA barcodes (rbcL, matK and ITS) indicates that R. mingii is a distinct lineage that genetically differs from R. genestierianum.
DOI: 10.15468/3wqf99
title: Lectotypification of the name Carex curvata Knaf (Cyperaceae) with some taxonomic remarks

description: This dataset contains the digitized treatments in Plazi based on the original journal article Řepka, Radomír, Więcław, Helena, Koopman, Jacob (2023): Lectotypification of the name Carex curvata Knaf (Cyperaceae) with some taxonomic remarks. Phytotaxa 592 (1): 68-72, DOI: 10.11646/phytotaxa.592.1.6, URL: http://dx.doi.org/10.1094/PDIS-04-22-0755-PDNAbstractA lectotype is designated for the name Carex curvata Knaf on a herbarium specimen found in the PR (National Museum, Prague). The specimen we selected seems to correspond to the author’s original concept of the name as supported by the herbarium label written by the author of the name and including the same locality as mentioned in the protologue. The typification is supplemented with taxonomic notes on the determination of similar and related species.
DOI: 10.15468/7t6heh
title: Neurocranial anatomy of Paralligator (Neosuchia: Paralligatoridae) from the Upper Cretaceous of Mongolia

description: This dataset contains the digitized treatments in Plazi based on the original journal article Kuzmin, Ivan T., Sichinava, Ekaterina A., Mazur, Evgeniia V., Gombolevskiy, Victor A., Sennikov, Andrey G., Skutschas, Pavel P. (2025): Neurocranial anatomy of Paralligator (Neosuchia: Paralligatoridae) from the Upper Cretaceous of Mongolia. Zoological Journal of the Linnean Society 203 (1): 1-40, DOI: 10.1093/zoolinnean/zlae177, URL: https://doi.org/10.1093/zoolinnean/zlae177
DOI: 10.15468/wknrnk
title: Cottus specus, a new troglomorphic species of sculpin (Cottidae) from southeastern Missouri

description: This dataset contains the digitized treatments in Plazi based on the original journal article Adams, Ginny L., Burr, Brooks M., Day, Julie L., Starkey, David E. (2013): Cottus specus, a new troglomorphic species of sculpin (Cottidae) from southeastern Missouri. Zootaxa 3609 (5): 484-494, DOI: 10.11646/zootaxa.3609.5.4AbstractCottus specus, a new species, is described from the karst regions of the Bois Brule drainage in eastern Missouri, USA. Cottus specus is distinguishable from all members of the genus Cottus using both genetic and morphological characters, including eye size and cephalic pore size. Cottus specus represents the first description of a cave species within Cottus. The addition of C. specus brings the total number of recognized species of Cottus to 33 in North American fresh waters.Key words: sculpin, cavefish, Cottus carolinae
DOI: 10.15468/ju6ap8
title: Lectotypification of Thalictrum chayuense (Ranunculaceae), with its reduction to the synonymy of T. tsawarungense, both described from Zayu in southeastern Xizang (Tibet), China

description: This dataset contains the digitized treatments in Plazi based on the original journal article Zeng, You-Pai, Yuan, Qiong, Yang, Qin-Er (2022): Lectotypification of Thalictrum chayuense (Ranunculaceae), with its reduction to the synonymy of T. tsawarungense, both described from Zayu in southeastern Xizang (Tibet), China. Phytotaxa 548 (2): 184-198, DOI: 10.11646/phytotaxa.548.2.4AbstractBased on critical observations on herbarium specimens (including type material) and living plants in the wild, we demonstrate that the holotype itself and the type collection of Thalictrum chayuense, which was described from Zayu county in southeastern Xizang (Tibet), China, are mixed, consisting of two taxa, T. chayuense and T. nepalense. Lectotypification is proposed for T. chayuense herein. Thalictrum chayuense is then determined to be conspecific with T. tsawarungense, a species described also from Zayu in southeastern Xizang. We therefore reduce T. chayuense to the synonymy of T. tsawarungense.