cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13828767
title: BOLD mtCOI database 2023-03-31 reformatted to SINTAX format for MB_Pipeline

description: Publicly available barcode records for the mitochondrial COI gene in the BOLD database (https://www.boldsystems.org/), release of 2023-03-31, reformatted to SINTAX format for the MB_Pipeline metabarcoding pipeline. The original data were released under a CC-BY-NC-SA license.

The conversion was performed with scripts from reformat-barcode-db (https://github.com/monagrland/reformat-barcode-db).  See log files for full command line and options used to filter sequences and prepare the HMMs. Different clustering, genetic code, and length parameters are required for each marker gene.

The Fasta files should be indexed to UDB format with Vsearch before use.

Description of files

All records:



bold.2023-03-31.coi-5p.all.fasta.gz - sequences in Fasta format, gzip compressed

bold.2023-03-31.coi-5p.all.log - log file for bold2sintax script

bold.2023-03-31.coi-5p.all.acc2bin - table of BIN identifiers for each accession, if available (else None)


European records only:



bold.2023-03-31.coi-5p.eur.fasta.gz - sequences in Fasta format, gzip compressed

bold.2023-03-31.coi-5p.eur.log - log file for bold2sintax script

european_countries.txt - List of country names used for subsetting

bold.2023-03-31.coi-5p.eur.acc2bin - table of BIN identifiers for each accession, if available (else None)


HMMer model for arthropod sequences:



bold.2023-03-31.coi-5p.arthropoda.hmm - HMM file

bold.2023-03-31.coi-5p.arthropoda.log - log file for bold2hmm script
DOI: 10.15468/dl.p7te65
title: Occurrence Download

description: A dataset containing 1211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Occurrence evidence, Material sample)",
 "Continent is one of (Asia, Europe, Africa, Antarctica, North America, Oceania, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Alternaria alternata (Fr.) Keissl.",
 "Year 2000-2024"
 ]
}

 The dataset includes 1211 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026769-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3886/e208744v1
title: ECIN Replication Package for "Parenthood and Occupational Mobility"

description: Replication files for "Parenthood and Occupational Mobility."
DOI: 10.15468/dl.tq3vgj
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Machilus austroguizhouensis S.K.Lee & F.N.Wei"
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026773-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6zhy3f
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Occurrence evidence)",
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Alternaria alternata (Fr.) Keissl.",
 "Year 2000-2024"
 ]
}

 The dataset includes 68 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026775-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nq94dm
title: Occurrence Download

description: A dataset containing 2249 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Barbus haasi Mertens, 1925"
 ]
}

 The dataset includes 2249 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026776-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s5g89a
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eriosyce calderana (F.Ritter) Ferryman"
 ]
}

 The dataset includes 26 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026777-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.4430627
title: EBSD datasets for cross-sectioned structural steel hardness indentations - Adaptive Domain Misorientation

description: Open access datasets for structural steel hardness indentations from the following publication: Ultramicroscopy 2021, Volume 222: https://doi.org/10.1016/j.ultramic.2021.113203

Files included:



Adaptive domain misorientation calculated for Indentation 1 and 2 using misorientation thresholds (Delta theta) 0.5deg and 2deg, corresponding to dense dislocation walls and sub-grain boundaries

Indentation 2: Raw dataset and associated mask file for excluding the edge of the data


The methodology for analysing and plotting of the data is found at: https://doi.org/10.5281/zenodo.4430623

For further information visit: Aalto University Wiki - https://wiki.aalto.fi/display/EMDIDS
DOI: 10.5281/zenodo.4430628
title: EBSD datasets for cross-sectioned structural steel hardness indentations - Adaptive Domain Misorientation

description: Open access datasets for structural steel hardness indentations from the following publication: Ultramicroscopy 2021, Volume 222: https://doi.org/10.1016/j.ultramic.2021.113203

Files included:



Adaptive domain misorientation calculated for Indentation 1 and 2 using misorientation thresholds (Delta theta) 0.5deg and 2deg, corresponding to dense dislocation walls and sub-grain boundaries

Indentation 2: Raw dataset and associated mask file for excluding the edge of the data


The methodology for analysing and plotting of the data is found at: https://doi.org/10.5281/zenodo.4430623

For further information visit: Aalto University Wiki - https://wiki.aalto.fi/display/EMDIDS
DOI: 10.15468/dl.8epjh7
title: Occurrence Download

description: A dataset containing 1211 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Material sample, Occurrence evidence)",
 "Continent is one of (Africa, Antarctica, Asia, Oceania, Europe, North America, South America)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Alternaria alternata (Fr.) Keissl.",
 "Year 2000-2024"
 ]
}

 The dataset includes 1211 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026778-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13711925
title: Files for the numerical results shown in "Far-from-equilibrium travelling pulses in sloped semi-arid environments driven by autotoxicity effects" by Gabriele Grifò, Annalisa Iuorio, and Frits Veerman

description: This folder contains the code used to produce Fig. 1 and Fig. 8-10 in the paper: "Far-from-equilibrium travelling pulses in sloped semi-arid environments driven by autotoxicity effects" by Gabriele Grifò, Annalisa Iuorio, and Frits Veerman. The preprint version of this paper is available at https://arxiv.org/abs/2405.1560.

In the subfolder "Direct_simulations", the code (to obtain Fig. 1) is based on a MATLAB routine which uses finite differences for spatial discretization with periodic boundary conditions together with MATLAB’s ode15s routine for time integration.

The continuation procedure (to obtain Fig. 8-10) is shown in the subfolder "Continuation" based on the software AUTO to analyse the dependence of the constructed travelling pulse solutions of Eq. (3.2) with respect to three system parameters, i.e. A, D, and H. Correspondingly, in each folder 'Continuation_X' where X=A, D, H, the results can be obtained by running the file 'AUTO_script_cont_X', based on the two files 'parab_X.f90' and 'c.parab_X'.

Selected solutions for each continuation are stored in the corresponding subfolders 'solutions_X', whereas the tables resulting from the continuation procedure in the scripts are shown in the files 'bifdiag_X.dat'. In each script file further details are provided in order to clarify how to extract the solutions used for the plots.
DOI: 10.5281/zenodo.13711926
title: Files for the numerical results shown in "Far-from-equilibrium travelling pulses in sloped semi-arid environments driven by autotoxicity effects" by Gabriele Grifò, Annalisa Iuorio, and Frits Veerman

description: This folder contains the code used to produce Fig. 1 and Fig. 8-10 in the paper: "Far-from-equilibrium travelling pulses in sloped semi-arid environments driven by autotoxicity effects" by Gabriele Grifò, Annalisa Iuorio, and Frits Veerman. The preprint version of this paper is available at https://arxiv.org/abs/2405.1560.

In the subfolder "Direct_simulations", the code (to obtain Fig. 1) is based on a MATLAB routine which uses finite differences for spatial discretization with periodic boundary conditions together with MATLAB’s ode15s routine for time integration.

The continuation procedure (to obtain Fig. 8-10) is shown in the subfolder "Continuation" based on the software AUTO to analyse the dependence of the constructed travelling pulse solutions of Eq. (3.2) with respect to three system parameters, i.e. A, D, and H. Correspondingly, in each folder 'Continuation_X' where X=A, D, H, the results can be obtained by running the file 'AUTO_script_cont_X', based on the two files 'parab_X.f90' and 'c.parab_X'.

Selected solutions for each continuation are stored in the corresponding subfolders 'solutions_X', whereas the tables resulting from the continuation procedure in the scripts are shown in the files 'bifdiag_X.dat'. In each script file further details are provided in order to clarify how to extract the solutions used for the plots.
DOI: 10.5281/zenodo.5054203
title: EBSD datasets for low-alloy steel weld metals - Arc, Laser, and Laser-hybrid welding

description: Example open access datasets for low-alloy structural steel weld metals, previously published in ref. [1]. The datasets are also related to the International Institute of Welding Commission C-IX, document nr. IX-L-1239-2021.

Files included:



The nomenclature of the files corresponds to what is used in ref. [1].

CV_3.crc/cpr: Conventional arc weld, 3/5 mm t-joint

HY_1.crc/cpr: Laser-hybrid weld, 3mm butt-joint

LA_1.crc/cpr: Laser weld, 3mm butt-joint


The methodology for analysing grain size and dislocation sub-structures is found at: https://zenodo.org/record/5053377 and https://doi.org/10.5281/zenodo.4430623

For further information visit: Aalto University Wiki - https://wiki.aalto.fi/display/GSMUM and https://wiki.aalto.fi/display/EMDIDS

Refererences:



[1] Materials Science and Engineering: A, 2014; 592: 28-39, http://dx.doi.org/10.1016/j.msea.2013.10.094

[2] Welding in the World. 2016; 60: 673-678. http://dx.doi.org/10.1007/s40194-016-0318-8

[3] Ultramicroscopy 2021, Volume 222, https://doi.org/10.1016/j.ultramic.2021.113203
DOI: 10.5281/zenodo.5054204
title: EBSD datasets for low-alloy steel weld metals - Arc, Laser, and Laser-hybrid welding

description: Example open access datasets for low-alloy structural steel weld metals, previously published in ref. [1]. The datasets are also related to the International Institute of Welding Commission C-IX, document nr. IX-L-1239-2021.

Files included:



The nomenclature of the files corresponds to what is used in ref. [1].

CV_3.crc/cpr: Conventional arc weld, 3/5 mm t-joint

HY_1.crc/cpr: Laser-hybrid weld, 3mm butt-joint

LA_1.crc/cpr: Laser weld, 3mm butt-joint


The methodology for analysing grain size and dislocation sub-structures is found at: https://zenodo.org/record/5053377 and https://doi.org/10.5281/zenodo.4430623

For further information visit: Aalto University Wiki - https://wiki.aalto.fi/display/GSMUM and https://wiki.aalto.fi/display/EMDIDS

Refererences:



[1] Materials Science and Engineering: A, 2014; 592: 28-39, http://dx.doi.org/10.1016/j.msea.2013.10.094

[2] Welding in the World. 2016; 60: 673-678. http://dx.doi.org/10.1007/s40194-016-0318-8

[3] Ultramicroscopy 2021, Volume 222, https://doi.org/10.1016/j.ultramic.2021.113203
DOI: 10.6084/m9.figshare.27088714
title: All_gene_sets_Ref.xlsx

description: gene sets related to epilepsy
DOI: 10.6084/m9.figshare.27088714.v1
title: All_gene_sets_Ref.xlsx

description: gene sets related to epilepsy
DOI: 10.15468/dl.zkqwaq
title: Occurrence Download

description: A dataset containing 97520836 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is iNaturalist Research-grade Observations"
 ]
}

 The dataset includes 97520836 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026768-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v9vhfj
title: Occurrence Download

description: A dataset containing 48675 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Squamata",
 "TaxonKey is Crocodylia",
 "TaxonKey is Testudines",
 "TaxonKey is Sphenodontia",
 "TaxonKey is Amphibia"
 ]
 },
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "and" : [
 "DecimalLongitude is greater than 52.197",
 "DecimalLongitude is less than 65.15",
 "DecimalLatitude is greater than -22.686",
 "DecimalLatitude is less than -15.645",
 "Country is Réunion"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 48675 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026779-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5517/ccdc.csd.cc2dph4r
title: CCDC 2225184: Experimental Crystal Structure Determination

description: Related Article: Shantanu Samanta, Debayan Sarkar|2023|ChemPhotoChem|7|e202200335|doi:10.1002/cptc.202200335
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gqfvh
title: CCDC 2285687: Experimental Crystal Structure Determination

description: Related Article: David Kočović, Berta Barta Holló, Ivana Borišev, Vukadin Leovac, Ljiljana Vojinović Ješić, Gerald Giester, Sergiu Shova, Zoran D. Tomić, Željko Jaćimović|2025|Inorg.Chim.Acta|574|122363|doi:10.1016/j.ica.2024.122363
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.15468/dl.3rtz8n
title: Occurrence Download

description: A dataset containing 1763 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "TaxonKey is Squamata",
 "TaxonKey is Crocodylia",
 "TaxonKey is Testudines",
 "TaxonKey is Sphenodontia",
 "TaxonKey is Amphibia"
 ]
 },
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "and" : [
 "DecimalLongitude is greater than 52.197",
 "DecimalLongitude is less than 65.15",
 "DecimalLatitude is greater than -22.686",
 "DecimalLatitude is less than -15.645",
 "Country is Mauritius"
 ]
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 1763 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0026780-240906103802322/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11209709
title: Replication data for: Stations of the Publicum Portorium Illyrici are a Strong Predictor of the Mithraic Presence in the Danubian Provinces: Geographical Analysis of the Distribution of the Roman Cult of Mithras

description: This repository serves as supplementary material for the article "Stations of the Publicum Portorium Illyrici are a Strong Predictor of the Mithraic Presence in the Danubian Provinces: Geographical Analysis of the Distribution of the Roman Cult of Mithras". This work was supported by the European Regional Development Fund project “Beyond Security: Role of Conflict in Resilience-Building” (reg. no.: CZ.02.01.01/00/22_008/0004595). The repository contains the following data:



Dataset for the evidence of the Roman cult of Mithras as collected by Ales Chalupa for the Roman provinces of Raetia, Noricum, Dalmatia, Regio X, Dalmatia, Pannonia, Moesia, Thracia. File: Mithras_AC.geojson

Geocoded Latin inscriptions collected from the LIST dataset (Vojtěch Kaše, Petra Heřmánková, & Adéla Sobotková. (2024). LIST (v1.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10473706) mentioning the deities Mithras, Minerva, Jupiter, Jupiter Dolichenus, Asclepius, Apollo, Mercury, Silvanus, Isis, Hercules in a csv format. Filename format: ListdeitynameWKTv1_2.csv.

Dictionary of noun forms for filtering deities Mithras, Minerva, Jupiter, Jupiter Dolichenus, Asclepius, Apollo, Mercury, Silvanus, Isis, Hercules in Latin inscriptions. File: deities_decline.csv

Spatial proximity analysis measurements. WEST_GEO_DIST(km) lists distances from Portorium West stations (N=11) to their nearest cult proxy in kilometers in geographical space; WEST_NET_DIST(m) lists distances from Portorium West stations (N=11) to their nearest cult proxy in meters across the transportation network of Roman roads; EAST_GEO_DIST(km) and EAST_NET_DIST(m) follow the same rationale for stations in the Portorium East group (N=16); NORICUM_DIST_NET_30(m) lists distances from Roman settlements in the province Noricum (and in the distance of 30 kilometers beyond the borders of Noricum) to their nearest cult proxy and portorium stations across the transportation network of Roman roads in meters (N=53). File: Distances.xlsx

Filtered Mithras_AC dataset with additional evidence from provinces neighboring Noricum for the purposes of correlation analysis. File: Mithras_AC_Noricum_neighbors.geojson

Results of Spearman correlation analysis for NORICUM_DIST_NET_30(m). File: NORICUM_RES_NET_30.csv

Geocoded Stations of the Publicum Portorium Illyrici. File: Portorium stations.csv

Portorium stations divided by administrative segments and attributed with periods based on Sarkisjan's dissertation. Files: Portorium_West_period.csv; Portorium_East_period.csv

Portorium members identified by inscriptions based on Sarkisjan's dissertation. File: Portorium_members.csv

The closest Mithraic evidence from the Mithras_AC to Portorium West and East stations with a chronological description. Files: mithras_ac_west_closest_period.csv; mithras_ac_east_closest_period.csv
DOI: 10.5281/zenodo.11209710
title: Replication data for: Stations of the Publicum Portorium Illyrici are a Strong Predictor of the Mithraic Presence in the Danubian Provinces: Geographical Analysis of the Distribution of the Roman Cult of Mithras

description: This repository serves as supplementary material for the article "Stations of the Publicum Portorium Illyrici are a Strong Predictor of the Mithraic Presence in the Danubian Provinces: Geographical Analysis of the Distribution of the Roman Cult of Mithras". This work was supported by the European Regional Development Fund project “Beyond Security: Role of Conflict in Resilience-Building” (reg. no.: CZ.02.01.01/00/22_008/0004595). The repository contains the following data:



Dataset for the evidence of the Roman cult of Mithras as collected by Ales Chalupa for the Roman provinces of Raetia, Noricum, Dalmatia, Regio X, Dalmatia, Pannonia, Moesia, Thracia. File: Mithras_AC.geojson

Geocoded Latin inscriptions collected from the LIST dataset (Vojtěch Kaše, Petra Heřmánková, & Adéla Sobotková. (2024). LIST (v1.2) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10473706) mentioning the deities Mithras, Minerva, Jupiter, Jupiter Dolichenus, Asclepius, Apollo, Mercury, Silvanus, Isis, Hercules in a csv format. Filename format: ListdeitynameWKTv1_2.csv.

Dictionary of noun forms for filtering deities Mithras, Minerva, Jupiter, Jupiter Dolichenus, Asclepius, Apollo, Mercury, Silvanus, Isis, Hercules in Latin inscriptions. File: deities_decline.csv

Spatial proximity analysis measurements. WEST_GEO_DIST(km) lists distances from Portorium West stations (N=11) to their nearest cult proxy in kilometers in geographical space; WEST_NET_DIST(m) lists distances from Portorium West stations (N=11) to their nearest cult proxy in meters across the transportation network of Roman roads; EAST_GEO_DIST(km) and EAST_NET_DIST(m) follow the same rationale for stations in the Portorium East group (N=16); NORICUM_DIST_NET_30(m) lists distances from Roman settlements in the province Noricum (and in the distance of 30 kilometers beyond the borders of Noricum) to their nearest cult proxy and portorium stations across the transportation network of Roman roads in meters (N=53). File: Distances.xlsx

Filtered Mithras_AC dataset with additional evidence from provinces neighboring Noricum for the purposes of correlation analysis. File: Mithras_AC_Noricum_neighbors.geojson

Results of Spearman correlation analysis for NORICUM_DIST_NET_30(m). File: NORICUM_RES_NET_30.csv

Geocoded Stations of the Publicum Portorium Illyrici. File: Portorium stations.csv