cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/8rgl5o
title: marine sediment metagenome Targeted loci environmental

description: Site U1387 offers a chance to study the response of microbial assemblage to specific seafloor events such as contourite depositions, changes in bottom current energy, shifts in organic matter deposition rates, and geochemical changes that are representative of seafloor processes during rapid climate change.
DOI: 10.15468/dl.u8qnqg
title: Occurrence Download

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

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008641-250920141307145/datasets/export for details.
DOI: 10.15468/zt9jb0
title: UCYN-A diversity in the Pacific

description: UCYN-A nifH amplicons were recovered from a coastal and oligotrophic site in the Pacific to characterize the diversity of UCYN-A sublineages.
DOI: 10.15468/kf1f9e
title: Comparative study in validity of three regions of 18S-rRNA for eukaryote amplicon sequence analyses

description: In the present study, we performed a detailed investigation of the 18S-rDNA, namely, numbers of registered sequences, frequencies of amplification success, the amplicon sequence variability among three regions containing V1-V3, V4-V5 and V7-V9 regions using in silico PCRs based on public databases, and the identification power by NGS-based environmental surveys of planktonic eukaryote community. Although the number of registered sequences in V4-V5 regions was remarkably higher than other regions, the identification power in NGS-based environmental surveys was lowest in V4-V5 regions due to the lowest sequence variability. The number of registered sequences in V1-V3 region was ca. two times smaller than V7-V9 region, and the sequence variability in V1-V3 region was significantly higher than that in V7-V9 region. Then, the identification power was not significant between these two regions, implying identification power is affected by combination of numbers of registered sequences and the sequence variability. We therefore believe V1-V3 region will be the best one for applying to NGS-based monitoring of planktonic eukaryote community in the near future as the number of sequences deposited increases in public databases.
DOI: 10.15468/aocrdi
title: soil metagenome Raw sequence reads

description: Profiling of Contaminated Soils in a Typical Antimony Mining Site
DOI: 10.15468/qh9vtx
title: Soil bacterial diversity is associated with human population density in urban greenspaces

description: Urban greenspaces form a vital part of the urban ecosystem and provide an extensive array of ecosystem services, including pollutant degradation, water management, carbon maintenance, and nutrient cycling. However, while the soil microbiota in these ecosystems are essential to these services they remain under-characterized. Here we aimed to determine whether turf grass soil bacterial communities were associated with human population density across a range of greenspaces in parks, streets, and residential areas across a major urban area. Results showed that bacterial diversity was significantly positively correlated with population density within the immediate vicinity of the sampled areas; and species diversity was greater in park and street soils, when compared with residential zones. Population density and greenspace type (park vs street vs residential area) also associated with the composition and structure of the bacterial community. Edaphic properties, including pH, moisture and texture, were also significantly correlated with microbial composition and structure. Co-occurrence network analysis revealed that microbial guilds in urban soils were well connected. Soil moisture and texture together with population density and greenspace type showed strong correlations with several network topological features including assortativity degree, edge density, average path, average betweenness and closeness. These results indicate that changes in urban demographics, as well as the changes in land-use may influence the diversity and structure of urban soil microbial communities. As urbanization is rapidly growing across the planet, understanding the consequences of different urban zoning on soil microbiota represents an unmet need.
DOI: 10.5281/zenodo.17182010
title: VitD and RBC count GWAS summary statistics and fine mapping results

description: UK Biobank vitamin D (VitD) and red blood cell (RBC) count GWAS summary statistics and SuSiE fine mapping results from the Kanai et al, 2021 preprint (https://doi.org/10.1101/2021.09.03.21262975). This is a mirror of the data for reproducibility purposes. Original files can be downloaded from Google Cloud.
DOI: 10.5281/zenodo.17182011
title: VitD and RBC count GWAS summary statistics and fine mapping results

description: UK Biobank vitamin D (VitD) and red blood cell (RBC) count GWAS summary statistics and SuSiE fine mapping results from the Kanai et al, 2021 preprint (https://doi.org/10.1101/2021.09.03.21262975). This is a mirror of the data for reproducibility purposes. Original files can be downloaded from Google Cloud.
DOI: 10.15468/dl.ug2qn2
title: Occurrence Download

description: A dataset containing 52 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphagnum ovatum"
 ]
}

 The dataset includes 52 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008642-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/ww62p1
title: Macroalgal Morphology affects composition and settlement of microbial communities

description: Macroalgae (seaweeds) have an intimate relationship with their microbial symbionts. Microbial communities associated with macroalgal surfaces (epibiota) are generally host-specific and, historically, there has been great interest in the role of biological compounds and chemical warfare in microbial community assembly on seaweeds. However, the interaction between seaweeds and their environment may also influence community assembly of their microbiota. In this experiment, I ask whether the interaction between water flow and seaweed morphology affects the settlement and structure of microbial biofilms. I test whether three common algal morphologies select for differential biofilm communities using artificial macro algae units (AM units) made out of latex. I find that morphology does affect initial microbial settlement and community structure, but that eventual dominance of substrate specialists (in our case, a latex degrader) swamps the influence of morphology in long-term biofilms.
DOI: 10.15468/dl.hzhdfz
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphagnum palustre pseudocymbifolium"
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008643-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6yexqc
title: Occurrence Download

description: A dataset containing 153 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphagnum palustre"
 ]
}

 The dataset includes 153 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008644-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/fgvndw
title: Ocean Acidification baceria sample Targeted loci environmental

description: A microcosm experiment was done in the western pacific ocean to investigate the response of bacterial community to the ocean acidification.
DOI: 10.15468/rex2oe
title: Microbiome (Bacteria, Archaea and fungi) from University Valley Permafrost cores (Antarctica)

description: Amplicon sequencing dataset (Bacteria and Archaea based on 16S ssu rRNA gene, Fungi and other eukaryotes, based on the ITS marker) of microorganisms in permafrost samples (two cores with three different depths) taken in University Valley, Antarctica.
DOI: 10.15468/dl.8fehwp
title: Occurrence Download

description: A dataset containing 230 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "OccurrenceStatus is Present",
 "TaxonKey is Picrodontidae"
 ]
}

 The dataset includes 230 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008645-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/fptojj
title: Diversity, Ecology and Biogeochemistry of cyst-forming acantharia (Radiolaria) in the oceans

description: Marine planktonic organisms that undertake active vertical migrations over their life cycle are important contributors to downward particle flux in the oceans. Acantharia, globally distributed heterotrophic protists that are unique in building skeletons of celestite (strontium sulfate), can produce reproductive cysts covered by a heavy mineral shell that sink rapidly from surface to deep waters. We combined phylogenetic and biogeochemical analyses to explore the ecological and biogeochemical significance of this reproductive strategy. Phylogenetic analysis of the 18S and 28S rRNA genes of different cyst morphotypes collected in different oceans indicated that cyst-forming Acantharia belong to three early diverging clades from the orders Chaunacanthida and Holacanthida that are mainly heterotrophic. Environmental high-throughput V9 tag sequences and clone libraries showed that the three clades are widely distributed in the Indian, Atlantic and Pacific Oceans at different latitudes, but seem more abundant in regions of higher primary productivity. Moreover, sequences of cyst-forming Acantharia were distributed evenly in both the photic and mesopelagic zone, a vertical distribution that we attribute to their life cycle where flagellated swarmers are released in deep waters from sinking cysts. Bathypelagic sediment traps in the subantarctic and oligotrophic subtropical Atlantic Ocean showed that downward flux of Acantharia was only large at high-latitudes and during a phytoplankton bloom. High organic carbon export in cold waters would be a putative nutritional source for non-symbiotic juveniles ascending in the water column. This study improves our understanding of the life cycle and biogeochemical contribution of Acantharia, and brings new insights into a remarkable reproductive strategy in marine protists
DOI: 10.15468/dl.ajyf67
title: Occurrence Download

description: A dataset containing 7321 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Magnolia Plum. ex L."
 ]
}

 The dataset includes 7321 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075939-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.17157054
title: Dataset for Microclimate Governs the Morphology of Sediment Flows on Mars

description: This dataset is volume 1/3 for the paper Microclimate Governs the Morphology of Sediment Flows on Mars
DOI: 10.5281/zenodo.17157055
title: Dataset for Microclimate Governs the Morphology of Sediment Flows on Mars

description: This dataset is volume 1/3 for the paper Microclimate Governs the Morphology of Sediment Flows on Mars
DOI: 10.15468/pogtfb
title: Raw sequence reads

description: Archaeal and bacterial 16S rRNA sequence from sediments sampled from Great Salt Lake, Utah, USA
DOI: 10.15468/dl.tvexfb
title: Occurrence Download

description: A dataset containing 76 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gleditsia australis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 76 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008646-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/oifcho
title: Marine metagenomes from the bioGEOTRACES project

description: Marine metagenomes from the bioGEOTRACES project Metagenome
DOI: 10.15468/ujycmm
title: Accuracy of protist diversity assessments: morphology compared to cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

description: Deep-sequencing technologies are becoming nearly routine to describe
 microbial community composition in environmental samples. 18S rDNA pyrosequencing
 has revealed a vast diversity of infrequent sequences, leading to the proposition of
 the existence of an extremely diverse microbial "rare biosphere". While rare
 microbes no doubt exist, critical views suggest that many rare sequences may
 actually be artifacts. However, information about how diversity revealed by
 molecular methods relates to that revealed by classical morphology approaches is
 practically non-existent. To address this issue, we used different approaches to
 assess the diversity of tintinnid ciliates, a species-rich group in which species
 can be easily distinguished morphologically. We studied two Mediterranean marine
 samples with different patterns of tintinnid diversity. We estimated tintinnid
 diversity in these samples employing morphological observations as well as both
 classical cloning and sequencing and pyrosequencing of two different markers, the
 18S rDNA and the ITS regions, applying a variety of computational approaches
 currently used to analyze pyrosequence reads. We found that both molecular
 approaches were efficient in detecting the tintinnid species observed by microscopy
 and revealed similar phylogenetic structures of the tintinnid community at the
 species level. However, depending on the method used to analyze the pyrosequencing
 results, we observed discrepancies with the morphology-based assessments up to
 several orders of magnitude. In several cases, the inferred number of operational
 taxonomic units (OTUs) largely exceeded the total number of tintinnid cells in the
 samples. Such inflation of the OTU numbers corresponded to "rare biosphere" taxa,
 composed largely of artefacts. Our results suggest that a careful and rigorous
 analysis of pyrosequencing datasets, including data denoising and sequence
 clustering with well-adjusted parameters, is necessary to accurately describe
 microbial biodiversity using this molecular approach.
DOI: 10.6084/m9.figshare.30185032
title: <i>mini</i>-N<sub><em>i</em></sub> : A small GC-MS database of nitrogen-containing compounds

description: <b><i>mini</i></b><b>-N</b><sub><i><strong>i</strong></i></sub><b> is a small database of electron ionization mass spectra and retention indices for nitrogen-containing compounds, mainly aromatic heterocycles.</b>Gas chromatography-mass spectrometry (GC-MS) is a very important method of chemical analysis. Identification is performed using a library search of the mass spectrum in a mass spectral database, and retention index information is also used. Nitrogen-containing small molecules with a high content of nitrogen (N<sub><em>i</em></sub> means <i>i</i> nitrogen atoms), such as derivatives of triazoles, pyrazoles, imidazoles, diazines, etc., including those containing -CN and -NH<sub>2</sub> groups, are an important class of analytes, including priority pollutants. Unfortunately, such compounds are insufficiently represented in the available GC-MS databases, and the databases also contain erroneous entries. This database partially fills this gap.All data (and further notes) are provided in an XLSX file. The other three files also contain mass spectra and retention indices, in formats suitable for import into NIST MS Search and other software. To import the SDF file into NIST MS Search, use the Lib2NIST utility.Electron ionization mass spectra and retention indices (5%-phenylpolydimethylsiloxane and polyethylene glycol) for 104 molecules are provided. For 72 molecules, retention indices are given for three different heating rates (temperature programming mode). The following chromatographic conditions were used for these molecules:<b>Non-polar stationary phase:</b><br>Column: 5%-phenyl-methylpolysiloxane, HP-5MS, 30m х 0.25mm х 0.50µm, Agilent; starting temperature 40 °C; helium flow rate 0.84 mL/min;<br><b>Polar stationary phase:</b><br>Column: polyethylene glycol, HP-INNOWax, 30m х 0.25mm х 0.25µm, Agilent; starting temperature 40 °C; helium flow rate 1.01 mL/min;The analyte solution in methanol (up to 10 analytes in one batch, concentration of each ~0.1 mg/mL) was injected using split injection mode (0.5 μL, 1:20). In some cases, the concentration was increased until high-quality mass spectra of sufficient intensity were obtained.Some of the retention index data was taken from the following source: Karnaeva A. E., Sholokhova A. Y. Validation of the identification reliability of known and assumed UDMH transformation products using gas chromatographic retention indices and machine learning //Chemosphere. – 2024. – V. 362. – P. 142679. https://doi.org/10.26434/chemrxiv-2024-mfbd6 (CC BY 4.0 license)All mass spectra were recorded using a Shimadzu GCMS-TQ8040 (quadrupole mass analyzer, 70 eV electron ionization mode). All mass spectra and retention indices were obtained using pure standards.<br>
DOI: 10.6084/m9.figshare.30185032.v1
title: <i>mini</i>-N<sub><em>i</em></sub> : A small GC-MS database of nitrogen-containing compounds

description: <b><i>mini</i></b><b>-N</b><sub><i><strong>i</strong></i></sub><b> is a small database of electron ionization mass spectra and retention indices for nitrogen-containing compounds, mainly aromatic heterocycles.</b>Gas chromatography-mass spectrometry (GC-MS) is a very important method of chemical analysis. Identification is performed using a library search of the mass spectrum in a mass spectral database, and retention index information is also used. Nitrogen-containing small molecules with a high content of nitrogen (N<sub><em>i</em></sub> means <i>i</i> nitrogen atoms), such as derivatives of triazoles, pyrazoles, imidazoles, diazines, etc., including those containing -CN and -NH<sub>2</sub> groups, are an important class of analytes, including priority pollutants. Unfortunately, such compounds are insufficiently represented in the available GC-MS databases, and the databases also contain erroneous entries. This database partially fills this gap.All data (and further notes) are provided in an XLSX file. The other three files also contain mass spectra and retention indices, in formats suitable for import into NIST MS Search and other software. To import the SDF file into NIST MS Search, use the Lib2NIST utility.Electron ionization mass spectra and retention indices (5%-phenylpolydimethylsiloxane and polyethylene glycol) for 104 molecules are provided. For 72 molecules, retention indices are given for three different heating rates (temperature programming mode). The following chromatographic conditions were used for these molecules:<b>Non-polar stationary phase:</b><br>Column: 5%-phenyl-methylpolysiloxane, HP-5MS, 30m х 0.25mm х 0.50µm, Agilent; starting temperature 40 °C; helium flow rate 0.84 mL/min;<br><b>Polar stationary phase:</b><br>Column: polyethylene glycol, HP-INNOWax, 30m х 0.25mm х 0.25µm, Agilent; starting temperature 40 °C; helium flow rate 1.01 mL/min;The analyte solution in methanol (up to 10 analytes in one batch, concentration of each ~0.1 mg/mL) was injected using split injection mode (0.5 μL, 1:20). In some cases, the concentration was increased until high-quality mass spectra of sufficient intensity were obtained.Some of the retention index data was taken from the following source: Karnaeva A. E., Sholokhova A. Y. Validation of the identification reliability of known and assumed UDMH transformation products using gas chromatographic retention indices and machine learning //Chemosphere. – 2024. – V. 362. – P. 142679. https://doi.org/10.26434/chemrxiv-2024-mfbd6 (CC BY 4.0 license)All mass spectra were recorded using a Shimadzu GCMS-TQ8040 (quadrupole mass analyzer, 70 eV electron ionization mode). All mass spectra and retention indices were obtained using pure standards.<br>
DOI: 10.15468/dl.5rud63
title: Occurrence Download

description: A dataset containing 43 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tanacetum corymbosum",
 "Country is Belgium",
 "HasCoordinate is true"
 ]
}

 The dataset includes 43 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008647-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/qtiebn
title: pyrosequencing Raw sequence reads of deep-sea Archaea

description: water-sediment interface in the slope Mariana Trench
DOI: 10.15468/jvmo2q
title: Coastal marsh sediment alkB, pmoA, and P450 gene survey

description: This dataset includes high-throughput amplicons for alkane dehydrogenase (alkB) genes, particulate monooxygenase (pmoA) genes, and cytochrome P450, encoded by CYP153, genes amplified and sequenced from subtidal sediment and inland soil samples collected biannually (September 2011 to October 2014) from a marsh near Grand Isle, Louisiana. This marsh was affected by oil deposition following the Deepwater Horizon oil spill in 2010. The goals of this dataset are to 1) track changes in the phylogenetic diversity of genes that code for a key enzymes used for bacterial alkane oxidation, short and long chain, from the oil impacted sediments and soil, and 2) to contribute to an understanding of bacterial functional role in the degradation of weathered oil residues in a natural marsh system.
DOI: 10.15468/dl.u8mjxb
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tanacetum corymbosum",
 "Country is Denmark",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008648-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/a2umj5
title: Chandeleur Island 2016 Amplicon Study Raw sequence reads

description: These amplicon sequences were generated from year 2 of an ongoing study of Chandeleur Islands saltmarsh habitats.
DOI: 10.15468/dl.5gnesn
title: Occurrence Download

description: A dataset containing 19 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Sphagnum teres"
 ]
}

 The dataset includes 19 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008650-250920141307145/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.