cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9qybxz
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((131.561 -0.623816, 131.490733 -0.629383, 131.422195 -0.645945, 131.357074 -0.673095, 131.296973 -0.710166, 131.243372 -0.756243, 131.197589 -0.8101930000000001, 131.160753 -0.870688, 131.133769 -0.936239, 131.117305 -1.005231, 131.111764 -1.075967, 131.117284 -1.146704, 131.133731 -1.215701, 131.160699 -1.281259, 131.197526 -1.341763, 131.243306 -1.395723, 131.29691 -1.441811, 131.357021 -1.47889, 131.422156 -1.506047, 131.490712 -1.522614, 131.561 -1.528182, 131.631288 -1.522614, 131.699844 -1.506047, 131.764979 -1.47889, 131.82509 -1.441811, 131.878694 -1.395723, 131.924474 -1.341763, 131.961301 -1.281259, 131.988269 -1.215701, 132.004716 -1.146704, 132.010236 -1.075967, 132.004695 -1.005231, 131.988231 -0.936239, 131.961247 -0.870688, 131.924411 -0.8101930000000001, 131.878628 -0.756243, 131.825027 -0.710166, 131.764926 -0.673095, 131.699805 -0.645945, 131.631267 -0.629383, 131.561 -0.623816))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 34 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037725-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26165/juelich-data/3zzuue
title: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-18

description: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-18Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2018-08-18'lightSource: Dark chamberprojectName: NO3IsoprenereactiveSpecies: NO3type: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.6084/m9.figshare.30821319
title: Achilles tendons of MRL/MpJ mice show scar-mediated healing after tenotomy

description: Tendon healing in Murphy Ross Large (MRL/MpJ) mice was examined using an Achilles tendon tenotomy model, a full transection model, to compare with previous studies in which regenerative tendon healing was shown in a patellar tendon focal injury model. Achilles tendons of MRL/MpJ and C57BL/6J mice were fully transected. Tensile testing and proteomics analysis were performed after four weeks of healing. MicroCT was performed after 10 weeks of healing. The Achilles tendons of MRL/MpJ mice healed via scar formation, regardless of sex, as did C57BL/6J mice. Tensile testing found that mechanical properties of injured tendons of both MRL/MpJ female and male mice were similar to those of C57BL/6J female and male mice, respectively, after four weeks of healing, which is during the remodeling phase. After 10 weeks of healing, injured tendons of MRL/MpJ mice possessed smaller heterotopic ossification volumes than those of C57BL/6J mice. Proteomics analysis revealed similar alterations to signaling pathways in injured tendons of MRL/MpJ and C57BL/6J male mice after four weeks of healing. However, among the altered pathways, actin cytoskeleton and integrin signaling pathways were two of the top pathways that were more prominently activated in C57BL/6J males than in MRL/MpJ males. These findings indicate that MRL/MpJ mice possess limited capacity to regenerate injured tendons after complete rupture, and that tenotomized Achilles tendons of MRL/MpJ male mice have lesser induction of heterotopic ossification and lower activation of the signaling pathways also induced with injury in C57BL/6J male mice.
DOI: 10.6084/m9.figshare.30821319.v1
title: Achilles tendons of MRL/MpJ mice show scar-mediated healing after tenotomy

description: Tendon healing in Murphy Ross Large (MRL/MpJ) mice was examined using an Achilles tendon tenotomy model, a full transection model, to compare with previous studies in which regenerative tendon healing was shown in a patellar tendon focal injury model. Achilles tendons of MRL/MpJ and C57BL/6J mice were fully transected. Tensile testing and proteomics analysis were performed after four weeks of healing. MicroCT was performed after 10 weeks of healing. The Achilles tendons of MRL/MpJ mice healed via scar formation, regardless of sex, as did C57BL/6J mice. Tensile testing found that mechanical properties of injured tendons of both MRL/MpJ female and male mice were similar to those of C57BL/6J female and male mice, respectively, after four weeks of healing, which is during the remodeling phase. After 10 weeks of healing, injured tendons of MRL/MpJ mice possessed smaller heterotopic ossification volumes than those of C57BL/6J mice. Proteomics analysis revealed similar alterations to signaling pathways in injured tendons of MRL/MpJ and C57BL/6J male mice after four weeks of healing. However, among the altered pathways, actin cytoskeleton and integrin signaling pathways were two of the top pathways that were more prominently activated in C57BL/6J males than in MRL/MpJ males. These findings indicate that MRL/MpJ mice possess limited capacity to regenerate injured tendons after complete rupture, and that tenotomized Achilles tendons of MRL/MpJ male mice have lesser induction of heterotopic ossification and lower activation of the signaling pathways also induced with injury in C57BL/6J male mice.
DOI: 10.6084/m9.figshare.29571083
title: Morphological and phylogenomic investigation of <i>Fistulifera</i> cf. <i>alcalina</i> (Naviculales, Stauroneidaceae) from the Transbaikalia (Southern Siberia, Russia) with comments on evolution within the genus

description: The genus <i>Fistulifera</i> Lange-Bert. (Bacillariophyceae, Naviculales, Stauroneidaceae) currently comprises five valid species, including predominantly small-celled species. We isolated a strain belonging to <i>Fistulifera</i> from the coastal sediment samples of saline Lake Zun-Torey in the Daursky Biosphere Reserve, Transbaikalia, Russia. It was attributed to <i>Fistulifera</i> cf. <i>alcalina</i> based on the study of live cells and frustule morphology using light and scanning electron microscopy, and processed for whole-genome short-read sequencing. We have conducted a phylogenetic study of <i>Fistulifera</i> using single genetic markers (18S nrDNA, <i>rbc</i>L) as well as mitogenome and plastome data. Despite the morphological data, the genetic study, especially mitogenomic results, suggests an independent species status for our strain. Our results challenge the hypothesis of the existence of an ‘alkaline clade’ inside the <i>Fistulifera</i> genus. In contrast to previous studies, we propose an independent origin of earlier derived ‘alkaline’ lineages. Moreover, our data have confirmed that <i>Fistulifera</i> is a sister group of <i>Proschkinia</i>.
DOI: 10.6084/m9.figshare.29571083.v1
title: Morphological and phylogenomic investigation of <i>Fistulifera</i> cf. <i>alcalina</i> (Naviculales, Stauroneidaceae) from the Transbaikalia (Southern Siberia, Russia) with comments on evolution within the genus

description: The genus <i>Fistulifera</i> Lange-Bert. (Bacillariophyceae, Naviculales, Stauroneidaceae) currently comprises five valid species, including predominantly small-celled species. We isolated a strain belonging to <i>Fistulifera</i> from the coastal sediment samples of saline Lake Zun-Torey in the Daursky Biosphere Reserve, Transbaikalia, Russia. It was attributed to <i>Fistulifera</i> cf. <i>alcalina</i> based on the study of live cells and frustule morphology using light and scanning electron microscopy, and processed for whole-genome short-read sequencing. We have conducted a phylogenetic study of <i>Fistulifera</i> using single genetic markers (18S nrDNA, <i>rbc</i>L) as well as mitogenome and plastome data. Despite the morphological data, the genetic study, especially mitogenomic results, suggests an independent species status for our strain. Our results challenge the hypothesis of the existence of an ‘alkaline clade’ inside the <i>Fistulifera</i> genus. In contrast to previous studies, we propose an independent origin of earlier derived ‘alkaline’ lineages. Moreover, our data have confirmed that <i>Fistulifera</i> is a sister group of <i>Proschkinia</i>.
DOI: 10.26165/juelich-data/5ezy58
title: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-16

description: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-16Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2018-08-16'lightSource: Dark chamberprojectName: NO3IsoprenereactiveSpecies: NO3type: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.5281/zenodo.17025330
title: Supplementary information for: PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content

description: This repository provides supplementary materials for the manuscript titled "PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content" [Ashkenazy and Weigel; 2025].

For each species analyzed in this study, we provide detailed results including the constructed pan-genome, phylogenetic trees, phyletic patterns, and all computed distances.

Repository Contents1. PanGeneOmeter_*_GCS_and_other_measures_pairs.csv ==> Contains all pairwise distances 2. *.PanX_geneClusters.txt.gz ==> Lists all genes with their corresponding assignments to orthology groups as determined by PanX, providing a comprehensive representation of the pan-genome structure.3. *.PanX.PhyleticPattern.01.csv ==> Provides the binary gene-content phyletic patterns (Presence/Absence) used for calculating GCSj and GCSo metrics and constructing the gene-content-based phylogenetic tree.4. *.IQ_Tree_BIN.treefile ==> The phylogenetic tree constructed based on the gene-content phyletic pattern5. *.SingleCopy_Core1_MSA_NT.IQ_tree.GTR_FR.treefile ==> The phylogenetic tree constructed based on the concatenated nucleotide Multiple Sequence Alignments (MSAs) of the core-genome.
DOI: 10.5281/zenodo.17025331
title: Supplementary information for: PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content

description: This repository provides supplementary materials for the manuscript titled "PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content" [Ashkenazy and Weigel; 2025].

For each species analyzed in this study, we provide detailed results including the constructed pan-genome, phylogenetic trees, phyletic patterns, and all computed distances.

Repository Contents1. PanGeneOmeter_*_GCS_and_other_measures_pairs.csv ==> Contains all pairwise distances 2. *.PanX_geneClusters.txt.gz ==> Lists all genes with their corresponding assignments to orthology groups as determined by PanX, providing a comprehensive representation of the pan-genome structure.3. *.PanX.PhyleticPattern.01.csv ==> Provides the binary gene-content phyletic patterns (Presence/Absence) used for calculating GCSj and GCSo metrics and constructing the gene-content-based phylogenetic tree.4. *.IQ_Tree_BIN.treefile ==> The phylogenetic tree constructed based on the gene-content phyletic pattern5. *.SingleCopy_Core1_MSA_NT.IQ_tree.GTR_FR.treefile ==> The phylogenetic tree constructed based on the concatenated nucleotide Multiple Sequence Alignments (MSAs) of the core-genome.
DOI: 10.15468/dl.cz4mzj
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Macellicephala laubieri",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 7 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037726-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26165/juelich-data/b0jm5o
title: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-15

description: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-15Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2018-08-15'lightSource: Dark chamberprojectName: NO3IsoprenereactiveSpecies: NO3type: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.15468/dl.dnb4eh
title: Occurrence Download

description: A dataset containing 114086 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((26.602708026244965 -27.218063902520722, 27.030643006071404 -27.218063902520722, 27.030643006071404 -26.820194985225736, 26.602708026244965 -26.820194985225736, 26.602708026244965 -27.218063902520722))"
 ]
}

 The dataset includes 114086 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037679-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17856422
title: Data of Automatically discovering heuristics in a complex SAT solver with large language models
DOI: 10.5281/zenodo.17856423
title: Data of Automatically discovering heuristics in a complex SAT solver with large language models
DOI: 10.5281/zenodo.17802334
title: Datasets supporting - Glacial Lake Observatory (GLO): A dataset of glacial lakes in Nepal and transboundary catchments (2017–2024)

description: Glacial Lake Observatory (GLO): Annual dataset of glacial lakes in Nepal and transboundary catchments (2017–2024)

Refer to the README.md for full details.
DOI: 10.5281/zenodo.17802333
title: Datasets supporting - Glacial Lake Observatory (GLO): A dataset of glacial lakes in Nepal and transboundary catchments (2017–2024)

description: Glacial Lake Observatory (GLO): Annual dataset of glacial lakes in Nepal and transboundary catchments (2017–2024)

Refer to the README.md for full details.
DOI: 10.26165/juelich-data/d82fki
title: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-14

description: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-14Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2018-08-14'lightSource: Dark chamberprojectName: NO3IsoprenereactiveSpecies: NO3type: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.15468/dl.b8hezr
title: Occurrence Download

description: A dataset containing 5308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "DecimalLatitude is greater than or equal to 69.085278",
 "DecimalLatitude is less than or equal to 74.085278",
 "DecimalLongitude is greater than or equal to 105.0",
 "DecimalLongitude is less than or equal to 110.0",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 5308 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037728-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.75dnpm
title: Occurrence Download

description: A dataset containing 15 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Azorella atacamensis, Azorella boelckei, Azorella burkartii, Azorella concolor, Azorella monteroi)",
 "BasisOfRecord is Specimen",
 "HasCoordinate is true"
 ]
}

 The dataset includes 15 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037730-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ff2n5k
title: Occurrence Download

description: A dataset containing 16130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Syncerus caffer",
 "HasCoordinate is TRUE"
 ]
}

 The dataset includes 16130 records from 70 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037727-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21227/3krk-nc14
title: "Interactional Chain-of-Thoughts Scene Graph Dataset"

description: "ICoT-SG dataset provides role-aware interaction scene graph annotations for compositional visual reasoning. Each scene contains hierarchical interaction graphs with explicit subject-object role differentiation. The dataset enables accurate reasoning about complex multi-object interactions, such as identifying active participants in crowded sports scenes."
DOI: 10.6084/m9.figshare.29756255
title: Raw data

description: This study is a network meta-analysis of the effects of different traditional Chinese exercises on lung cancer patients. The results were obtained through the search and statistical analysis of multiple databases, aiming to understand the differences in the therapeutic effects of different traditional Chinese exercises.
DOI: 10.6084/m9.figshare.29756255.v1
title: Raw data

description: This study is a network meta-analysis of the effects of different traditional Chinese exercises on lung cancer patients. The results were obtained through the search and statistical analysis of multiple databases, aiming to understand the differences in the therapeutic effects of different traditional Chinese exercises.
DOI: 10.6084/m9.figshare.29756255.v2
title: Raw data

description: This study is a network meta-analysis of the effects of different traditional Chinese exercises on lung cancer patients. The results were obtained through the search and statistical analysis of multiple databases, aiming to understand the differences in the therapeutic effects of different traditional Chinese exercises.
DOI: 10.26165/juelich-data/wk9ga6
title: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-13

description: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-13Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2018-08-13'lightSource: Dark chamberprojectName: NO3IsoprenereactiveSpecies: NO3type: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.21227/yrr2-y460
title: "Interactional Chain-of-Thoughts Scene Graph Dataset"

description: "ICoT-SG dataset provides role-aware interaction scene graph annotations for compositional visual reasoning. Each scene contains hierarchical interaction graphs with explicit subject-object role differentiation. The dataset enables accurate reasoning about complex multi-object interactions, such as identifying active participants in crowded sports scenes."
DOI: 10.18738/t8/qavrsp
title: Supplementary data : Stratified epithelium

description: This dataset contains the raw multi-angle lensfree microscopy measurements of a thin stratified epithelium tissue section, along with the LED calibration and acquisition metadata required for reconstruction. Only raw measurements and calibration files are included.
DOI: 10.15468/dl.x7q74d
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"within","geometry":"POLYGON ((-79.608 -0.620816, -79.67826700000001 -0.626383, -79.74680499999999 -0.642945, -79.811925 -0.670095, -79.87202600000001 -0.707166, -79.925628 -0.753243, -79.971411 -0.807193, -80.008247 -0.867688, -80.03523 -0.933239, -80.051695 -1.002231, -80.057236 -1.072967, -80.051715 -1.143704, -80.035269 -1.212701, -80.00830000000001 -1.278259, -79.971473 -1.338763, -79.92569399999999 -1.392723, -79.872089 -1.438811, -79.81197899999999 -1.47589, -79.746844 -1.503047, -79.67828799999999 -1.519614, -79.608 -1.525182, -79.537712 -1.519614, -79.469156 -1.503047, -79.404021 -1.47589, -79.34391100000001 -1.438811, -79.290306 -1.392723, -79.24452700000001 -1.338763, -79.2077 -1.278259, -79.18073099999999 -1.212701, -79.16428500000001 -1.143704, -79.15876400000001 -1.072967, -79.164305 -1.002231, -79.18077 -0.933239, -79.207753 -0.867688, -79.244589 -0.807193, -79.290372 -0.753243, -79.343974 -0.707166, -79.40407500000001 -0.670095, -79.469195 -0.642945, -79.537733 -0.626383, -79.608 -0.620816))"},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037731-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.26165/juelich-data/zq14ru
title: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-12

description: isoprene + NO3 - Gas-phase oxidation - product study - 2018-08-12Chamber information:actris_nf: Yinstitute: FZJlink: https://www.eurochamp.org/simulation-chambers/SAPHIRname: SAPHIRvolume: 270 m3wallMaterial: FEP filmExperimental conditions:date: '2018-08-12'lightSource: Dark chamberprojectName: NO3IsoprenereactiveSpecies: NO3type: Gas-phase oxidation - product studyMolecules:- name: isoprene
DOI: 10.48420/30449888
title: Supplementary Material and raw data for “Bar-seq analysis of Aspergillus fumigatus kinome library during infection of airway epithelial cells”

description: To investigate the role of Aspergillus fumigatus genes encoding for protein kinase functions, we infected A549 alveolar epithelial cells with a pool of 111 A. fumigatus barcoded null mutants in genes encoding protein kinases and utilised bar-seq to identify which of these are involved in survival within A549 cells. This folder contains:<i>Underlying data</i>Earle F1000 Gate Away Data.xls (raw data for figures).<i>Extended data</i>Earle F1000 Supplementary Figures.pdf (Supplementary Figures 1 & 2)Earle F1000 Code Deseq2.txt (R code for Deseq2 analysis)Earle F1000 Code Volcano Plot.txt (R code to do Volcano plots shown in Supplementary Figure 2)Earle F1000 Code Heatmap.txt (R code to do Heatmap as shown in Figure 1)Earle F1000 Code get_txt IDs for genes of interest (R code to get IDs for genes of interest)Earle F1000 kinasebc.txt (list of barcodes for individual deletion mutants in the kinase library)Earle F1000 Code get counts.txt (R code to retrieve gene counts)