cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.9t2zd5
title: Occurrence Download

description: A dataset containing 593 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Mamíferos voladores laguna El Tinije"
 ]
}

 The dataset includes 593 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077234-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.suqjc2
title: Occurrence Download

description: A dataset containing 105 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Stoeberia beetzii (Dinter) Dinter & Schwantes"
 ]
}

 The dataset includes 105 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0108083-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d87b9q
title: Occurrence Download

description: A dataset containing 1054355 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Egretta tricolor (Statius Muller, 1776))",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Machine Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 1054355 records from 148 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016275-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tz2xz6
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Alchemilla austroaltaica V.N.Tikhom."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008080-230224095556074/datasets/export for details.
DOI: 10.15468/dl.ax6ap2
title: Occurrence Download

description: A dataset containing 168 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus matitanensis Leandri"
 ]
}

 The dataset includes 168 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0077240-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4ak2a6
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Wurfbainia mindanaensis (Elmer) Škorničk. & A.D.Poulsen"
 ]
}

 The dataset includes 14 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019942-230224095556074/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.p875pn
title: Occurrence Download

description: A dataset containing 25193 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Adonis vernalis L."
 ]
}

 The dataset includes 25193 records from 262 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0033297-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18419/darus-3307/71
title: ICRS@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/12
title: LNK@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/23
title: LNK@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/39
title: LNK@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/52
title: LNK@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/10
title: LNK@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/1
title: LNK@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/42
title: NAND@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/64
title: NAND@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/36
title: NOR@manual-v1do.json

description: :unav
DOI: 10.18419/darus-3307/45
title: NAND@manual-v1_optimized.json

description: :unav
DOI: 10.18419/darus-3307/56
title: NAND@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/72
title: NOR@manual-v1do_simple.pdf

description: :unav
DOI: 10.18419/darus-3307/44
title: NOR@manual-v1.json

description: :unav
DOI: 10.1285/i20705948v12n4p774
title: Student mobility in higher education: Sicilian outflow network and chain migrations

description: The Italian public universities are subsidised within a competitive framework that awards excellence, efficiency, and the capacity of universities to attract students from Italian regions other than its own. However, repeated cuts to public spending has increased the well-known Italian North-South divide. The most important student mobility (SM) flow is from the Southern to the Central-Northern regions--a phenomenon that has been magnified by an increasing number of outgoing students from Sicily over the last decade. In this paper, we rely upon micro-data of university enrolment and students' personal records for three cohorts of freshmen, in order to investigate preferential patterns of SM from Sicily toward universities in other regions. Indeed, our main goal is to eventually reveal the existence of chain migrations, through which students from a particular geographical area move towards a particular destination. We consider 38 clusters aggregating the 390 Sicilian municipalities, based on geographical proximity and socio-economic criteria. The data from each cohort is represented as a tripartite network with three sets of nodes, namely, clusters of Sicilian municipalities, students, and universities. The tripartite network is projected in a bipartite weighted network of clusters and universities, which is, then, filtered, in order to obtain a statistically validated bipartite network (SBVN). The SBVNs of the three cohorts suggest the existence and evolution of chain migration patterns over time, which are also gender specific.
DOI: 10.18419/darus-3307/27
title: NOR@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/30
title: NOR@manual-v1_optimized_simple.pdf

description: :unav
DOI: 10.18419/darus-3307/40
title: NOR@manual-v1_optimized.json

description: :unav
DOI: 10.18419/darus-3307/6
title: NOR@manual-v1_optimized.json

description: :unav
DOI: 10.18419/darus-3307/74
title: NOR@manual-v2do.json

description: :unav
DOI: 10.48597/evuh-4hyn
title: Measurement of OC/EC at Peyrusse Vieille

description: Measurement of OC/EC at Peyrusse Vieille
DOI: 10.18419/darus-3307/34
title: NOR@manual-v2.json

description: :unav
DOI: 10.18419/darus-3307/46
title: NOR@manual-v2_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/50
title: NOR@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/59
title: NOR@manual-v2_optimized_simple.pdf

description: :unav
DOI: 10.18419/darus-3307/67
title: NOR@manual-v2_optimized.json

description: :unav
DOI: 10.18419/darus-3307/68
title: NOR@manual-v2do_simple.pdf

description: :unav
DOI: 10.18419/darus-3307/16
title: NOT@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/25
title: NOT@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/28
title: NOT@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/48
title: OR@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/49
title: NOR@manual-v2.pdf

description: :unav
DOI: 10.18419/darus-3307/21
title: OR@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/24
title: NOR@manual-v2_optimized.json

description: :unav
DOI: 10.18419/darus-3307/11
title: OR@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/63
title: TOR_SQ_2x2.json

description: :unav
DOI: 10.18419/darus-3307/35
title: TOR_SQ_2x2.pdf

description: :unav
DOI: 10.18419/darus-3307/2
title: TOR_SQ_UC@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/8
title: TOR_SQ_UC@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/26
title: TOR_SQ_UC@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/3
title: TOR_SQ_UC@manual-v1_optimized.json

description: :unav
DOI: 10.18419/darus-3307/41
title: TOR_SQ_UC@manual-v1_optimized_simple.pdf

description: :unav
DOI: 10.18419/darus-3307/14
title: TOR_SQ_UC@manual-v1_simple.pdf

description: :unav
DOI: 10.18419/darus-3307/22
title: XNOR@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/38
title: XNOR@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/53
title: TOR_SQ_UC@manual-v1_optimized.json

description: :unav
DOI: 10.18419/darus-3307/57
title: XNOR@manual-v1.pdf

description: :unav
DOI: 10.18419/darus-3307/62
title: XOR@manual-v1_optimized.json

description: :unav
DOI: 10.18419/darus-3307/69
title: XOR@manual-v1.json

description: :unav
DOI: 10.18419/darus-3307/7
title: XOR@manual-v1_manifold.pdf

description: :unav
DOI: 10.18419/darus-3307/73
title: TOR_SQ_UC@manual-v1.pdf

description: :unav
DOI: 10.3334/cdiac/spruce.007
title: SPRUCE S1 Bog Pretreatment Photosynthesis and Respiration for Black Spruce: 2010-2013
DOI: 10.25505/fiz.icsd.cc2p869h
title: CSD 2480536: Experimental Crystal Structure Determination

description: Related Article: K. Moon, Y. Ding, H. Okrepka, R. Wu, C.N. Ewald, P. Yadav, A. Biswas, E. Harel, M. Kuno, S. Kim|2025|ACS Nano|19||doi:10.1021/acsnano.5c14651
description: An entry from the Inorganic Crystal Structure Database, the world’s repository for inorganic crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the joint CCDC and FIZ Karlsruhe Access Structures service and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.7910/dvn/bgvihx
title: Replication data for: The Power of Tests for Detecting p-Hacking

description: Review of Economics and Statistics: Forthcoming.
description: Volume XX, Issue X
DOI: 10.3334/cdiac/spruce.019
title: SPRUCE S1 Bog Fine-root Production and Standing Crop Assessed With Minirhizotrons in the Southern and Northern Ends of the S1 Bog

description: Fine roots contribute to ecosystem carbon, water, and nutrient fluxes through resource acquisition, respiration, exudation, and turnover, but are understudied in peatlands. This data set reports fine-root peak growth and standing crop measurements from a forested, ombrotrophic bog as determined using non-destructive minirhizotron technology. Minirhizotron images were collected throughout the growing seasons of 2011 and 2012 at the southern and northern ends of the S1 bog across gradients of tree density in paired hummock and hollow microtopography. The dominant woody species in the bog, and focus of the investigation, were trees Picea mariana and Larix laricina, and ericaceous shrubs <em>Rhododendron groenlandicum</em> and <em>Chamaedaphne calyculata</em>. The data were derived from minirhizotron images where root length and diameter were measured on ~weekly images and used to calculate: (1) Annual fine-root production and peak standing crop in 2011 and 2012; (2) Seasonal fine-root phenology throughout the growing seasons of 2011 and 2012; and (3) The distribution of newly-produced fine-root length throughout the peat profile in 2011 and 2012. The measurements were made in the S1 Bog, a Picea mariana [black spruce] – Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF). These minirhizotron images were collected prior to the construction of the SPRUCE experimental plots.
DOI: 10.3334/cdiac/spruce.022
title: SPRUCE S1 Bog Plant-Available Nutrients Assessed with Ion-Exchange Resins from 2011-2012 in the Southern End of the S1 Bog

description: This data set consists of observations of plant-available nutrients assessed using ion-exchange resin capsules incubated serially in aerobic and anaerobic peat layers beginning in 2011. Data were collected from 2011 to 2012 (prior to the construction of the SPRUCE experimental plots) at the southern end of the S1 Bog at three depths in hollow microtopography only. The experimental work was conducted in a Picea mariana [black spruce] – Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).
DOI: 10.3334/cdiac/spruce.023
title: SPRUCE S1 Bog Areal Coverage of Hummock and Hollow Microtopography Assessed Along Three Transects in the S1 Bog

description: Aerial coverage of hummocks and hollows was estimated in July 2012 in ten 4 m × 4 m plots each along three 60-m transects in the S1 Bog. Hollows were defined as the lowest elevation within plots and were typically at or near the height of the water table, hummocks included area above hollows, including the sides of the hummocks. The experimental work was conducted in a Picea mariana [black spruce] – Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).
DOI: 10.3334/cdiac/spruce.024
title: SPRUCE S1 Bog Tree Basal Area and Understory Community Composition Assessed in the Southern and Northern Ends of the S1 Bog

description: The composition and cover of woody and understory species, along with the timing of stem growth, were characterized near minirhizotron installations at the south and north ends of the S1 bog in order to understand the relationship between root dynamics and the surrounding plant communities. There are three data streams: (1) Woody species basal area -- the number, basal area, and distance from the center point of all trees within a 5-m radius of each minirhizotron pair, which were quantified in 2011, (2) Understory cover -- the understory vascular plant community composition and percent cover, which were surveyed in 1 m2 areas at four cardinal directions adjacent to each pair of minirhizotrons in June 2011, and (3) Stem growth -- the basal area increment (stem growth) of nearby trees, which was quantified using automated or manual dendrobands in 2011 and 2012, respectively. The measurements were made in the S1-Bog of the Marcell Experimental Forest (MEF) near Grand Rapids, Minnesota.
DOI: 10.3334/cdiac/spruce.025
title: SPRUCE S1 Bog Pretreatment Fungal Hyphae Carbon and Nitrogen Concentrations and Stable Isotope Composition from In-growth Cores, 2013-2014

description: This data set provides fungal hyphal carbon and nitrogen concentrations and stable isotopic composition data for samples obtained from the S1 Bog. Hyphae were collected using 40 μm in-growth bags (10 cm × 10 cm) filled with sterile sand. Bags were incubated in the field in paired hummock and hollows at six locations in the bog at three depths and two topographic positions. In hummocks, bags were inserted at +10 to 0 cm above the adjacent hollow and in both locations from 0 to -10 cm and -10 to -20 cm below the hollow surface. All measurements were made at the 8.1-ha S1 bog forest site in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).
DOI: 10.5281/zenodo.17541635
title: A catalog of genes and species of the human skin microbiota

description: Dataset overviewThis dataset provides:a non-redundant high-quality catalog of 2.9 million genes392 Metagenomic Species Pangenomes (MSPs)This dataset can be used to analyze shotgun sequencing data of the human skin microbiota.
How to use this datasetCreate a gene abundance table by aligning reads from each sample against the catalog. For this purpose, you can use Meteor or NGLess. Then, normalize raw counts by gene length.Taxonomic profiling: the abundance of each species can be estimated as the average abundance of its 100 first core genes. To reduce the false positive rate, only consider that a species is present if at least 10/100 marker genes are detected.
Methods
Data sourcesThis dataset was built using the following data sources:118 isolate-derived genomes from the HMRGD246 isolate-derived genomes from the Skin Microbial Genome Collection (SMGC)1,407 skin metagenome assemblies from the Skin Microbial Genome Collection (SMGC)
Non-redundant gene catalogAfter filtering out short contigs (<1500 bp), genes were predicted with Prodigal on genomes (mode: single) and metagenome assemblies (mode: meta). Complete genes (partial=00) were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
Functional annotationKOs assignments were obtained with KofamScan using the KEGG 107 database.
MSPs recoveryReads from the 1,120 skin metagenomes available in the bioproject PRJNA46333 were aligned against the non-redundant gene catalog with the Meteor software suite to produce a raw gene abundance table (2.9M genes quantified in 1,120samples). Then, co-abundant genes were binned in 392 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationTaxonomic annotation was performed by alignment of all core and accessory genes against representative genomes of the GTDB database (release r214) using blastn (version 2.7.1, task = megablast, word_size = 16). A species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean nucleotide identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs (or the corresponding genome if available) with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJNA46333 (cohort used in catalogue assembly) and PRJEB80549 (independent cohort not used in assembly).
DOI: 10.5281/zenodo.17541600
title: Updated Metagenomic Species Pan-genomes (MSPs) of the human gastrointestinal microbiota

description: Gene catalog constructionThe methodology for creating the IGC2 catalog is described in the original papers: Li et al., 2014 and Wen et al., 2017
MSP creationReads from publicly available human gut metagenomes were aligned against the IGC2 catalog with the Meteor to produce a raw gene abundance table (10.4M genes quantified in >2000 samples). Then, co-abundant genes were binned in 1,989 Metagenomic Species Pan-genomes (MSPs, i.e. clusters of co-abundant genes that likely belong to the same microbial species) using MSPminer.
MSPs taxonomic annotationMSPs taxonomic annotation was performed by aligning MSP core and accessory genes against representative genomes of the Genome Taxonomy Database (GTDB r207) using blastn (task = megablast, word_size = 16). The 20 best hits for each gene were kept (--max-target-seq 20). Using an in-house pipeline, a species-level assignment was given if > 50% of the genes matched the representative genome of a given species, with a mean identity ≥ 95% and mean gene length coverage ≥ 90%. The remaining MSPs were assigned to a higher taxonomic level (genus to superkingdom), if more than 50% of their genes had the same annotation.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the MSPs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni). 
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB1786, PRJEB5224, PRJEB6337, PRJNA422434 (cohort used in catalogue assembly) and PRJEB11532, PRJEB33500, PRJEB37249, PRNJNA834801 (independent cohort not used in assembly).
DOI: 10.3334/cdiac/spruce.038
title: SPRUCE Pretreatment Plant Tissue Analyses, 2009 through 2013

description: This data set reports the results of elemental analyses of foliar and stem/woody twig plant tissues collected at the SPRUCE site in 2009, 2012, and 2013. Samples were obtained at various locations around the S1 Bog and from within the developing experimental treatment plots. These are pretreatment vegetation samples, collected prior to initiation of the SPRUCE experiment heating and elevated CO2 treatments. The experimental work was conducted in a Picea mariana [black spruce] – Sphagnum spp. bog forest in northern Minnesota, 40 km north of Grand Rapids, in the USDA Forest Service Marcell Experimental Forest (MEF).
DOI: 10.5281/zenodo.17541526
title: MetaChick: characterization of the chicken caecal metagenome by deep shotgun sequencing

description: Data sourcesThis dataset was constructed using the samples of the MetaChick project (phase 1) corresponding to the cecal content of 340 animals. Sequencing data and associated metadata have been submitted to INSDC (bioproject: PRJEB38174).
Sequencing data QC and metagenomic assemblyFirst, sequencing adapters removal and read trimming was performed with fastxtend. Reads mapped on the host genome (GRCg7b GCA_016699485.1) with bowtie2 were removed with samtools. Finally, metagenomic assembly was performed with metaSPAdes v3.14.1. Contigs of less than 1500 bp were removed.
MAGs recoveryMAGs were generated with MetaBAT 2 (multi-coverage mode) and MAGs quality was assessed with CheckM. MAGs with completeness < 70% or contamination > 5% or N50 < 8Kb were discarded. Pairwise Average Nucleotide Identity (ANI) was computed for all recovered MAGs with fastANI and dereplication at species level (ANI cutoff = 95%).
Non-redundant gene catalogGenes were predicted on all contigs from metagenomic assemblies with Prodigal (parameters : -m -p meta). Genes were pooled and clustered with cd-hit-est (parameters -c 0.95 -aS 0.90 -G 0 -d 0 -M 0 -T 0) by choosing those from the longest contigs as representatives.
MSPs recoveryA raw gene abundance table (13,6M genes quantified in 340 samples) was generated with meteorMeteor. Then, co-abundant genes were binned in Metagenomic Species Pan-genomes (MSPs, i.e. gene clusters that likely belong to the same microbial species) using MSPminer.
MAGs and MSPs taxonomic annotationDereplicated MAGs were annotated with GTDB-Tk based on GTDB r214. Then, MAGs taxonomic annotation was propagated to the corresponding MSPs.
Construction of the phylogenetic tree39 universal phylogenetic markers genes were extracted from the dereplicated MAGs with fetchMGs. Then, the markers were separately aligned with MUSCLE. The 40 alignments were merged and trimmed with trimAl (parameters: -automated1). Finally, the phylogenetic tree was computed with FastTreeMP (parameters: -gamma -pseudo -spr -mlacc 3 -slownni).
Mapping rate distribution across public cohortsWe generated mapping rate distribution plots using Meteor2 (default parameters), comparing performance between: PRJEB38174 (cohort used in catalogue assembly) and PRJEB29033, PRJEB33338, PRJEB53667 (independent cohort not used in assembly).