cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.70dn712/9
title: Figure 7 code

description: This file includes the code used to create one of the panels in Figure 7. It includes the life cycle loop iterated over multiple generations, for different parameter values.
DOI: 10.5061/dryad.cb8gd26/10
title: ExaML phylogenomic tree

description: ExaML topology from phylogenomic data, used as a constraint for the GenBank supermatrix tree search. Node labels represent bootstrap frequencies.
DOI: 10.5061/dryad.cb8gd26/11
title: Concatenated matrix -- phylogenomic data

description: Concatenated matrix for phylogenomic data. The matrix has been rearranged so that codon positions are in consecutive partitions.
DOI: 10.5061/dryad.cb8gd26/12
title: Partition file for phylogenomic data

description: Partition file for phylogenomic data. Partitions represent consecutive codon positions.
DOI: 10.5061/dryad.cb8gd26/13
title: Concatenated supermatrix -- GenBank data

description: Concatenated GenBank data supermatrix.
DOI: 10.5061/dryad.cb8gd26/14
title: Partition file for GenBank supermatrix

description: Partition file for GenBank supermatrix. Partitions represent gene boundaries.
DOI: 10.5061/dryad.cb8gd26/6
title: Niche phyloPCA PC1 -- BEAST congruified

description: First axis of phyloPCA of environmental data using BEAST congruified tree.
DOI: 10.5061/dryad.cb8gd26/7
title: Trait phyloMDS PC1 -- BEAST congruified

description: First axis of phyloMDS of trait data using BEAST congruified tree.
DOI: 10.5061/dryad.cb8gd26/8
title: Niche phyloPCA PC1 -- treePL

description: First axis of phyloPCA of environmental data using treePL tree.
DOI: 10.5061/dryad.cb8gd26/9
title: Trait phyloMDS PC1 -- treePL

description: First axis of phyloMDS of trait data using treePL tree.
DOI: 10.5061/dryad.f32p4/57
title: RAD-seq raw reads Swertia_site21-2
DOI: 10.5061/dryad.f32p4/58
title: RAD-seq raw reads Swertia_site21-3
DOI: 10.5061/dryad.f32p4/59
title: RAD-seq raw reads Swertia_site23-2
DOI: 10.5061/dryad.f32p4/60
title: RAD-seq raw reads Swertia_site23-1
DOI: 10.5061/dryad.f32p4/61
title: RAD-seq raw reads Swertia_site24-1
DOI: 10.5061/dryad.f32p4/62
title: RAD-seq raw reads Swertia_site24-2
DOI: 10.5061/dryad.f32p4/63
title: RAD-seq raw reads Swertia_site23-3-1

description: SjaRAD3_IPd012_ctgggccg-1.fastq.zip needs to be combined with SjaRAD3_IPd012_ctgggccg-2.fastq.zip
DOI: 10.5061/dryad.f32p4/64
title: RAD-seq raw reads Swertia_site23-3-2

description: SjaRAD3_IPd012_ctgggccg-2.fastq needs to be combined with SjaRAD3_IPd012_ctgggccg-1.fastq
DOI: 10.5061/dryad.f32p4/65
title: RAD-seq raw reads Patrinia_site3-1
DOI: 10.5061/dryad.f374gf0/1
title: ADH alignment file

description: Nexus format file for ADH gene alignment
DOI: 10.5061/dryad.f374gf0/2
title: GLO

description: Nexus format alignment file for GLO
DOI: 10.5061/dryad.f374gf0/3
title: GS

description: Nexus format alignment file for GS
DOI: 10.5061/dryad.f374gf0/4
title: ITS

description: Nexus format alignment file for ITS
DOI: 10.5061/dryad.qm8b161/1
title: Figuresnew
DOI: 10.5061/dryad.s0b85c2/2
title: testAullophalus
DOI: 10.5061/dryad.s7j17qp/1
title: Parser Extraction of Triples in Unstructured Text

description: The web contains vast repositories of unstructured text. We investigate the opportunity for building a knowledge graph from these text sources. We generate a set of triples which can be used in knowledge gathering and integration. We define the architecture of a language compiler for processing subject-predicate-object triples using the OpenNLP parser. We implement a depth-first search traversal on the POS tagged syntactic tree appending predicate and object information. A parser enables higher precision and higher recall extractions of syntactic relationships across conjunction boundaries. We are able to extract 2-2.5 times the correct extractions of ReVerb. The extractions are used in a variety of semantic web applications and question answering. We verify extraction of 50,000 triples on the ClueWeb dataset.
DOI: 10.5061/dryad.sd69mc7/10
title: FigS3

description: Figure S3. Biogeography of Tetraglochin species and their climatic niches along the environmental (E) space. Left: ancestral range estimation (ARE) on the Tetraglochin chronogram using the DEC model in BioGeoBEARS. States at nodes (squares) represent the area with highest ML probability before the instantaneous speciation event, whereas those on branches represent the state of the descendant lineage immediately after speciation. Squares with more than one letter refer to ancestral areas composed of more than one biogeographical area. Boxes to the left of taxon names indicate areas of tip species. Probabilities of ancestral areas are shown to the right of nodes. Right: Climatic niches for species of Tetraglochin produced by the three main axes of the PCA-env. For each species, the gray to black shading represents the grid cell density of the species occurrence (black being the highest density). The dashed line represents 50% of the available environment and the solid line represents 100%.
DOI: 10.5061/dryad.sd69mc7/11
title: FigS4

description: Figure S4. Results from the niche comparisons between Tetraglochin species in the environmental (E) space. Niche overlap estimations among Tetraglochin  species using the first three axes of the PCA-env. A. PCs 1-2. B. PCs 1-3. C. PCs 2-3. For A-C, left: pairwise niche overlap between each Tetraglochin species quantified using the Schoener’s D index, right: agglomerative hierarchical clustering UPGMA algorithm using niche overlap estimations. SA: Southern Andean distribution; CA: Central Andean distribution; SA-CA:  Southern and Central Andean distribution.
DOI: 10.5061/dryad.sd69mc7/12
title: FigS5

description: Figure S5.  Bar plots of niche breadth and geographical range size values for Tetraglochin species. Niche breadth for each species was estimated as the sum of its variances on the first three principal components obtained in the PCA-env method. Geographical range size was estimated from binary (presence/absence) distributions maps for each Tetraglochin species derived from the SDM and using the maximum training sensitivity plus specificity as threshold.
DOI: 10.5061/dryad.sd69mc7/13
title: FigS6

description: Figure S6. Results from the species distribution modelling (SDM) for Tetraglochin species. Maps show predicted suitable climatic conditions (logistic output) from the MaxEnt model for the six species of Tetraglochin, using BIO1 (Annual Mean Temperature), BIO2 (Mean Diurnal Range), BIO3 (isothermality), BIO4 (temperature seasonality), BIO9 (Mean Temperature of Driest Quarter), BIO12 (annual precipitation), BIO19 (Precipitation of Coldest Quarter), and PET (potential evapotranspiration) as climatic variables. Dots represent specimen occurrences used for the SDM analyses.
DOI: 10.5061/dryad.sd69mc7/14
title: FigS7

description: Figure S7. Ancestral climatic tolerances plotted on the MCC species tree for variables analyzed in the geographical (G) space. Interior nodes represent the mean of estimated ancestral climatic tolerances using maximum likelihood and 100 random samples from the predicted niche occupancy (PNO) profiles. The 80 % density interval of climatic tolerances is indicated by a vertical dashed line, and the mean is indicated by the taxon label. BIO1: Annual Mean Temperature, BIO2: Mean Diurnal Range, BIO3: isothermality, BIO4: temperature seasonality, BIO9: Mean Temperature of Driest Quarter, BIO12: annual precipitation, BIO19: Precipitation of Coldest Quarter, and PET: potential evapotranspiration).
DOI: 10.5061/dryad.sd69mc7/15
title: FigS8

description: Figure S8. Biplot of the first two principal components extracted in the phylogenetic principal component analyses (pPCA) using the weighted means of the PNOs for each species and environmental variables. BIO1: Annual Mean Temperature, BIO2: Mean Diurnal Range, BIO3: isothermality, BIO4: temperature seasonality, BIO9: Mean Temperature of Driest Quarter, BIO12: annual precipitation, BIO19: Precipitation of Coldest Quarter, and PET: potential evapotranspiration).
DOI: 10.5061/dryad.sd69mc7/16
title: FigS9

description: Figure S9. Binary (presence/absence) distributions maps for Tetraglochin species derived from the SDM outputs using the maximum training sensitivity plus specificity as threshold.
DOI: 10.5061/dryad.sd69mc7/7
title: Tetraglochin_1000trees_pruned

description: 1000 randomly subsampled posterior trees from the Bayesian species tree analyses in BEAST v1.8.2 using ribosomal ITS and the chloroplast trnL-F, pruned to include only the species of Tetraglochin.
DOI: 10.5061/dryad.sd69mc7/8
title: FigS1

description: Figure S1. Distribution map of Tetraglochin and delimited area corresponding to the 50 km-buffered minimum convex polygon used in the niche analyses both along the environmental (E) and geographical (G) space.
DOI: 10.5061/dryad.sd69mc7/9
title: FigS2

description: Figure S2.Results from the climatic niche analyses in the space environmental (E) space obtained using the PCA-env method. Left: Correlation circles showing the contribution of environmental variables on the first three axes of the PCA-env and the percentage of inertia explained. Right:  PCAenv scatterplots of the first three principal components based on 21 climatic variables for the six Tetraglochin species represented by 388 occurrences.
DOI: 10.15159/phytop.16
title: Lake Peipsi 2003 (Phytoplankton samples)

description: Method: Phytoplankton samples were preserved in Lugol’s (acidified iodine) solution and counted under an inverted microscope (Utermöhl, 1958). 3 ml of preserved sample was settled overnight and counted in random fields or transects. Biovolumes of algal cells, colonies and/or filaments were calculated using assigned geometric shapes dimensions, and converted to biomass assuming the specific density of 1 g cm-3 in accordance with Edler (1979). Approved by CEN on 14 July 2006 “Water quality - Guidance standard on the enumeration of phytoplankton using inverted microscopy (Utermöhl technique)” (CEN 15204, 2006) European Standard EN 15204:2006 Utermöhl, H., 1958. Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitteilungen der Internationale Vereinigung für Theoretische und Angewandte Limnologie 9, 1- 38. Edler, L. (ed.), 1979. Recommendations on methods for marine biological studies in the Baltic Sea. Phytoplankton and chlorophyll. Baltic Marine Biologists WG 9.
DOI: 10.17632/32r487xp5v.1
title: Ticker Price Comparison Post IPO for Two Flash Storage Startups

description: Trended stock price post IPO for two hot flash storage companies
DOI: 10.17632/3r7xmmh6gz.1
title: Data for: 3371802

description: регрессионный анализ данных
DOI: 10.17632/3y3ny73pcs.1
title: Data for: Agricultural extension, intra-household allocation and malaria

description: Data and code to replicate "Agricultural extension, intra-household allocation and malaria"
DOI: 10.17632/55svc4nhvd.1
title: Data for: Regional risk assessment of debris flows in China—an HRU-based approach

description: This is the basic data of our research in this manuscript. 1) Debris flows, basin boundary,rain gauges in in Longxi River Basin; 2) Hazard-forming factors of debris flows.
DOI: 10.17632/ndjyw2vnym.1
title: Data for: High-throughput thermodynamic calculations of phase equilibria in solidified 6016 Al-alloys

description: The calculated phase equilibria information for 6016 alloys
DOI: 10.17632/pfkr82j6sr.1
title: Data for: 3371794

description: regression analysis of data
DOI: 10.17632/pfkr82j6sr.2
title: Data for: 3371794

description: regression analysis of data
DOI: 10.17632/pfkr82j6sr.3
title: Data for: 3371794

description: regression analysis of data
DOI: 10.17632/scrdwnzc7t.1
title: Data for: Analysis of Critical Incidents in Tunnels to Improve Collective Activity and Learning from Experience

description: table of tunnel patrollers critical incidents
DOI: 10.17632/x5v9mk72y5.1
title: Data for: Dental microwear texture analysis of Pliocene Suidae from Hadar and Kanapoi in the context of early hominin dietary breadth expansion

description: Raw dental microwear texture data of modern African suid species and fossil suids from the eastern African Pliocene sites of Kanapoi and Hadar.
DOI: 10.5061/dryad.26036h6/1
title: Length measurements for P1 conodont elements and their space / time context

description: Length measurement for P1 elements were obtained from the bibliography (references in table), using measurement tool from the GIMP software. All studied material were complete enough that total length could be measured. data associated to each element include genera and species name, presence of a 'platform' morphology, the reference, the stratigraphic context as defined in the reference and the geographic location of the specimen collection. NB: Coordinates are for the most part VERY approximate, and are not raw data from the reference, but our estimation based on what information the original authors gave.
DOI: 10.5061/dryad.29h669c/1
title: Data from: Fitness of an allopolyploid rupicolous fern compared to its diploid progenitors: From sporogenesis to sporophyte formation
DOI: 10.5061/dryad.2g1f4n5/18
title: NEWICKS 2

description: Newick formatted  trees.
DOI: 10.5061/dryad.2g1f4n5/19
title: Pycnogonium_littorale_SAMN10093767

description: Transcriptome assembly
DOI: 10.5061/dryad.2g1f4n5/20
title: Lithobius_atkinsoni_SAMN10093766
DOI: 10.5061/dryad.59j72f2/1
title: Data for Mago/Matinta phylogeny (16SND1 gene and gene trees)

description: 16SND1 data used to demonstrate the relationship among amycines, along with resulting phylogenetic trees.
DOI: 10.5061/dryad.61sr186/1
title: Data of the results of SPOMSIM modeling

description: Features of the 15 species and 15 streets for which population dynamics was modeled and SPOMSIM modeling results.
DOI: 10.5061/dryad.c3269fc/1
title: BeadData

description: Raw images of the experiments for bead accumulation in macrophage
DOI: 10.5061/dryad.c3269fc/2
title: LipidData

description: Raw images of the experiments for lipid accumulation in macrophages
DOI: 10.5061/dryad.cb8gd26/15
title: Mean latitudes per species

description: Species latitude data for trait-associated diversification analysis.
DOI: 10.5061/dryad.cb8gd26/16
title: Biogeographic data

description: Biogeographic data for trait-associated diversification analysis.
DOI: 10.5061/dryad.cb8gd26/17
title: Mean elevation per species

description: Species elevation data for trait-associated diversification analysis.
DOI: 10.5061/dryad.cb8gd26/18
title: Saxifragales floristic traits

description: Matrix with Saxifragales traits extracted from floras.
DOI: 10.5061/dryad.cb8gd26/19
title: Extracted environmental data

description: Extracted Saxifragales environmental data. Each variable is stored in a different file; for a guide to variable numbering see the excel sheet in this deposition.
DOI: 10.5061/dryad.cb8gd26/20
title: Guide to variable numerical coding

description: Guide to variable numerical coding.
DOI: 10.15156/bio/sh1262510.08fu
title: SH1262510.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.25549/one-c4-54947
title: Documents
DOI: 10.15156/bio/sh1262511.08fu
title: SH1262511.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1262512.08fu
title: SH1262512.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1262513.08fu
title: SH1262513.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1262514.08fu
title: SH1262514.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1262515.08fu
title: SH1262515.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1262516.08fu
title: SH1262516.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1262517.08fu
title: SH1262517.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.