cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1174072.10fu
title: SH1174072.10FU

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: 10.15468/dl.y4n9fj
title: Occurrence Download

description: A dataset containing 92804 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Psittacula krameri (Scopoli, 1769)",
 "Country is Netherlands",
 "Year is greater than or equal to 1500"
 ]
}

 The dataset includes 92804 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047090-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wae798
title: Occurrence Download

description: A dataset containing 3225 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Zungaro zungaro (Humboldt, 1821), Pseudoplatystoma tigrinum (Valenciennes, 1840), Piaractus brachypomus (Cuvier, 1818), Prochilodus nigricans Spix & Agassiz, 1829, Colossoma macropomum (Cuvier, 1816), Brachyplatystoma filamentosum (Lichtenstein, 1819), Brachyplatystoma platynemum Boulenger, 1898, Brachyplatystoma juruense (Boulenger, 1898), Brachyplatystoma rousseauxii (Castelnau, 1855))",
 "BasisOfRecord is one of (Human Observation, Observation, Machine Observation, Living Specimen, Specimen)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than or equal to 1000",
 "CoordinateUncertaintyInMeters is null"
 ]
 },
 "OccurrenceStatus is one of (Present)"
 ]
}

 The dataset includes 3225 records from 77 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047091-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s3w9fk
title: Occurrence Download

description: A dataset containing 1106014 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-58.49742 -16.93902,-53.45816 -16.93902,-53.45816 -13.1196,-58.49742 -13.1196,-58.49742 -16.93902))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 1106014 records from 459 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047089-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.28082405.v1
title: Association of domain-specific physical activity with nocturia: a population-based study

description: Nocturia is the most prevalent lower urinary tract symptom (LUTS) and is closely associated with various diseases and social burdens. Research on the relationship between physical activity and various diseases has progressed significantly. However, the association between nocturia and physical activity has received limited attention in prior studies. Thus，this study aimed to investigate the relationship between different domains of physical activity (e.g., occupation-related physical activity [OPA], transportation-related physical activity [TPA], and leisure-time physical activity [LTPA]) and nocturia. We included 5516 participants from the cross-sectional National Health and Nutrition Examination Survey (NHANES) conducted between 2007 and 2012，employing survey-weighted logistic regression, restricted cubic splines (RCS), subgroup analysis, and sensitivity analysis to assess the relationship between different domains of physical activity and nocturia.<b> </b>Multivariable logistic regression analysis revealed a significant negative correlation between PA, LTPA, and nocturia. Specifically, PA (OR: 0.7523, 95% CI: 0.6307–0.8974, P = 0.002) and LTPA (OR: 0.7664, 95% CI: 0.6314–0.9304, P = 0.007) were negatively associated with nocturia. The RCS curve demonstrated non-linear relationships between PA, LTPA, and nocturia. Additionally, subgroup analyses and sensitivity analyses further validated this association.<b> </b>Based on this cross-sectional study, we suggested that PA and LTPA are associated with a reduced risk of nocturia in adults aged 20 years and older in the United States. This underscoring the importance of physical activity in preventing and managing nocturia may provide valuable guidance for clinical practice.
DOI: 10.15468/dl.erhkyy
title: Occurrence Download

description: A dataset containing 34258 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Animal Sound Archive"
 ]
}

 The dataset includes 34258 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047093-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/vcf5f2k5yb.1
title: Custom scripts for "Advanced Complexity and Plasticity of Neural Activity in Reciprocally Connected Human Cerebral Organoids"

description: As an organoid model for a long-range neuronal circuitry, we investigated neuronal activity of two separate cerebral organoids reciprocally connected by axons. Strikingly, the connected organoids produced significantly more intense and complex oscillatory activity than conventional or directly fused two cerebral organoids. The axonal connections also promoted developmental maturation in a distinct cellular population of the organoids. The connected organoids could follow periodic external stimuli and exhibit complex patterns of plasticity as a macroscopic neuronal network. These results demonstrated that axonal projections not just simply transmit signals, but rather enhance complexity and functional maturity of the cerebral organoids. This study supports the idea that the inter-regional connections within brains are the key structures for generating functional complexity. It thus paves a way for investigating development and functions of macroscopic neuronal circuits in vitro.
DOI: 10.17632/vcf5f2k5yb.3
title: Custom scripts for "Advanced Complexity and Short-Term Plasticity of Neural Activity in Reciprocally Connected Human Cerebral Organoids"

description: As an organoid model for a long-range neuronal circuitry, we investigated neuronal activity of two separate cerebral organoids reciprocally connected by axons. Strikingly, the connected organoids produced significantly more intense and complex oscillatory activity than conventional or directly fused two cerebral organoids. The axonal connections also promoted developmental maturation in a distinct cellular population of the organoids. The connected organoids could follow periodic external stimuli and exhibit complex patterns of plasticity as a macroscopic neuronal network. These results demonstrated that axonal projections not just simply transmit signals, but rather enhance complexity and functional maturity of the cerebral organoids. This study supports the idea that the inter-regional connections within brains are the key structures for generating functional complexity. It thus paves a way for investigating development and functions of macroscopic neuronal circuits in vitro.
DOI: 10.17632/vcf5f2k5yb.2
title: Custom scripts for "Advanced Complexity and Plasticity of Neural Activity in Reciprocally Connected Human Cerebral Organoids"

description: As an organoid model for a long-range neuronal circuitry, we investigated neuronal activity of two separate cerebral organoids reciprocally connected by axons. Strikingly, the connected organoids produced significantly more intense and complex oscillatory activity than conventional or directly fused two cerebral organoids. The axonal connections also promoted developmental maturation in a distinct cellular population of the organoids. The connected organoids could follow periodic external stimuli and exhibit complex patterns of plasticity as a macroscopic neuronal network. These results demonstrated that axonal projections not just simply transmit signals, but rather enhance complexity and functional maturity of the cerebral organoids. This study supports the idea that the inter-regional connections within brains are the key structures for generating functional complexity. It thus paves a way for investigating development and functions of macroscopic neuronal circuits in vitro.
DOI: 10.15468/dl.jrhpxz
title: Occurrence Download

description: A dataset containing 767 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-3.22434 4.8861,7.27464 4.8861,7.27464 11.74036,-3.22434 11.74036,-3.22434 4.8861))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Chlorocebus Gray, 1870",
 "Year 2015-2024"
 ]
}

 The dataset includes 767 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047095-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/3zcx3xdgp5.1
title: Corpus of Transparent Peer Review

description: The Corpus of Transparent Peer Review is a comprehensive dataset compiled from the transparent peer review reports of research articles published in Nature Communications. Nature Communications, a leading journal in the field of Science, encompasses a broad spectrum of disciplines, including Physical, Earth and Environmental Sciences, Biological Sciences, and Health Sciences. This dataset offers insights into the transparent peer review process, shedding light on the rigorous evaluation and collaborative efforts that contribute to the publication of high-quality scientific research.

Dataset Overview:

Source Journal: Nature Communications
Major Knowledge Domains: Biological Sciences and Physical Sciences
Number of Articles: 560 (280 from BS & 280 from PS)
Number of Reviewer Reports: 596 Reviewer Reports in BS & 607 Reviewer Reports PS of 280 published articles
Number of Author Responses: 529 Author Responses Reports in BS & 531 Author Responses Reports PS

Transparent Peer Review Process:
The dataset includes peer review reports that have been made transparent and publicly available since January 2016. The transparent peer review system adopted by Nature Communications involves the publication of both reviewers' comments and authors' point-by-point responses. The process typically starts with Round 1, where reviewers provide comments on the submitted article. Authors then have the opportunity to respond to these comments, initiating an interactive and collaborative process. Depending on the initial reviews and the revisions made by the authors, the article may undergo subsequent peer review rounds, ensuring a thorough and iterative improvement of the manuscript.

The primary objective of providing transparent peer review reports is to enhance the objectivity of the peer review process and inform potential applicants about the expected standards of the journal. This dataset can enable researchers to conduct genre analysis in the area of transparent peer review, contributing to a deeper understanding of the collaborative efforts between reviewers and authors to enhance the quality of scientific publications.

***Earlier Research benefitting from Corpus of Transparent Peer Review includes:

** Sönmez, D. (2021). ''It would be helpful if the authors could clarify …'': A pragmatic analysis of transparent peer reviews (Thesis No: 700911) [MA Thesis, Erciyes University]. National Thesis Center. https://tez.yok.gov.tr/UlusalTezMerkezi

** Tekin, M. (2021). A move analysis of transparent peer reviews as an academic genre: Exploring reviewers' comments (Thesis No: 704810) [MA Thesis, Erciyes University]. National Thesis Center. https://tez.yok.gov.tr/UlusalTezMerkezi

** Sönmez, D., & Akbas, E. (2023). ‘Great work folks!’: establishing interpersonal communication in transparent peer reviews of research articles . Ibérica, (46), 69–95. https://doi.org/10.17398/2340-2784.46.69
DOI: 10.15468/dl.4hsh3n
title: Occurrence Download

description: A dataset listing the 14210 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungal Biodiversity Centre (CBS) - Fungi strains"
 ]
}

 The dataset's 14210 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047092-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12571070
title: Subtypes of chromatin topologically associated domains in mouse embryonic stem cell

description: TAD_types.bed: The chromatin coordinates of six subtypes of TADs

TAD_ChIP_strength_fpkm_size_E1_interaction_twoborerexpression_innerfpkm.tsv: TAD annotated with ChIP_seq signals, TAD strength, gene expression inside TADs, TAD size, PC1 values, interaction frequency between borders, gene expression on the borders

border_type_states.tsv: TAD border coordinates, annotated with the type classification, and the 12 chromatin states inferred with ChromHMM

chromatinstates_description.tsv: the biological description of the chromatin states E1-E12
DOI: 10.15468/dl.y8r6qw
title: Occurrence Download

description: A dataset containing 1852 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acanthus ilicifolius L."
 ]
}

 The dataset includes 1852 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047094-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ryau4a
title: Occurrence Download

description: A dataset containing 49459 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungal Biodiversity Centre (CBS) - Fungi strains"
 ]
}

 The dataset includes 49459 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047096-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6b5djm
title: Occurrence Download

description: A dataset containing 390 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Engystomops coloradorum (Cannatella & Duellman, 1984)"
 ]
}

 The dataset includes 390 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047098-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ez7dhy
title: Occurrence Download

description: A dataset containing 49459 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Fungal Biodiversity Centre (CBS) - Fungi strains"
 ]
}

 The dataset includes 49459 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047099-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.26104624
title: Tectonic evolution of the Madawara greenstone belt, southern Bundelkhand craton, central India: a window to see the Meso- to Neoarchaean geodynamics

description: The Palaeo- to Neoarchaean Bundelkhand Craton (BkC) in central India has received attention due to its felsic crust evolution. There are two linear patches of relict greenstone belts in the BkC, and the central greenstone belt has been the focus of extensive research for the past two decades. In contrast, the southern greenstone belt has received inadequate attention. At the southern BkC, the E-W Madawara Greenstone Belt is represented by patches of remnant mantle serpentinites and metasedimentary rocks that are tectonically juxtaposed with Archaean basement TTG gneisses and Proterozoic Bijawar Group of rocks. This study highlights key findings from fields, geological maps, petrography, and a large number of whole rock chemical analyses of serpentinites and spinel chemistry to unravel the tectonic evolution story. We identified two serpentinites with contrasting petrological and geochemical properties: spinel peridotite (SP) and talc-tremolite schist (TTS). SP is primarily dunite to harzburgite with relatively high MgO (33 wt%), enriched Yb, and shows strong re-fertilization. TTS, on the other hand, is lherzolitic and less refractory (MgO = 25 wt%). Chemically, these two serpentinites were mantle wedge and subducted peridotites, respectively. The unaltered cores of the chromium spinels represent a fore-arc setting. These findings, in conjunction with prior research, paint a compelling picture of a Neoarchaean (~2.5 Ga) subduction system once present in the southern Bundelkhand Craton. The serpentinites represent relict ophiolites – from a northerly dipping trench. It also explains a Mesoarchaean rift basin system between the two cratonic nuclei of southern Bundelkhand, which amalgamated during the Kenorland Supercontinent formation.
DOI: 10.6084/m9.figshare.26104624.v1
title: Tectonic evolution of the Madawara greenstone belt, southern Bundelkhand craton, central India: a window to see the Meso- to Neoarchaean geodynamics

description: The Palaeo- to Neoarchaean Bundelkhand Craton (BkC) in central India has received attention due to its felsic crust evolution. There are two linear patches of relict greenstone belts in the BkC, and the central greenstone belt has been the focus of extensive research for the past two decades. In contrast, the southern greenstone belt has received inadequate attention. At the southern BkC, the E-W Madawara Greenstone Belt is represented by patches of remnant mantle serpentinites and metasedimentary rocks that are tectonically juxtaposed with Archaean basement TTG gneisses and Proterozoic Bijawar Group of rocks. This study highlights key findings from fields, geological maps, petrography, and a large number of whole rock chemical analyses of serpentinites and spinel chemistry to unravel the tectonic evolution story. We identified two serpentinites with contrasting petrological and geochemical properties: spinel peridotite (SP) and talc-tremolite schist (TTS). SP is primarily dunite to harzburgite with relatively high MgO (33 wt%), enriched Yb, and shows strong re-fertilization. TTS, on the other hand, is lherzolitic and less refractory (MgO = 25 wt%). Chemically, these two serpentinites were mantle wedge and subducted peridotites, respectively. The unaltered cores of the chromium spinels represent a fore-arc setting. These findings, in conjunction with prior research, paint a compelling picture of a Neoarchaean (~2.5 Ga) subduction system once present in the southern Bundelkhand Craton. The serpentinites represent relict ophiolites – from a northerly dipping trench. It also explains a Mesoarchaean rift basin system between the two cratonic nuclei of southern Bundelkhand, which amalgamated during the Kenorland Supercontinent formation.
DOI: 10.6084/m9.figshare.26047707
title: Early Paleozoic tectonic evolution in the central Vietnam: evidence from geochronological and geochemical constraints

description: Magmatic rocks distributed along the western part of the Po Ko fault, which documented tectono-thermal evolution of the Indochina block, when and how they formed are less constrained. Our new geochronological and geochemical data reveal that they were generated at 488–457 Ma and display a variety of SiO<sub>2</sub> concentrations (SiO<sub>2</sub> = 50.7–72.8 wt%). They also generally show slightly negative Eu anomalies (Eu/Eu* = 0.65–0.98) and enrich in LILEs (e.g. Rb and K) but deplete in HFSEs (e.g. Nb and Ta), consistent with arc-related signatures. Combined with their relatively high Mg# values (Mg# = 56–40) and initial<sup>87</sup>Sr/<sup>86</sup>Sr ratios (0.7085–0.7167) but negative εNd(t) values (−2.5 to −3.7), we consider those magmatic rocks originated from an enriched mantle source (e.g. EMII), which was metasomatized in the past. In comparing our data with tectono-thermal events in the southern Truong Son belt, we infer that there existed an ocean (a branch of the proto-Tethys Ocean) between the Truong Son belt and the Kontum massif during Late Cambrian, which subsequently underwent southeast subduction beneath the Kontum mass if initiated at ~488 Ma and terminated at ~457 Ma.
DOI: 10.6084/m9.figshare.26124858
title: Oligocene magmato-tectonic events influential in the development of Pb-Zn, Ag, and Au mineralization at the Plomosas deposit, southwestern Sierra Madre Occidental, Mexico

description: The Plomosas deposit is the product of a sequence of overlapping events of Pb–Zn, Ag, and Au low sulfidation mineralization that occurred in Mexico’s southwestern Sierra Madre Occidental (SMO). Field observations, detailed petrography, and U–Pb age dating of the entire stratigraphic sequence were used to characterize the magmatic evolution of the district and to obtain new insights into the evolution of the SMO. The stratigraphy at Plomosas is distinct from other areas to the north as it lacks Jurassic marine units, Cretaceous continental volcanic successions as well as Cretaceous and Palaeocene batholiths. The local basement is composed of undeformed Late Jurassic volcaniclastic units and coeval felsic intrusions. Early to late Oligocene silicic ignimbrites, intermediate lava flows, and occasional basaltic flows unconformably overlie the Jurassic basement. Several Oligocene intermediate to felsic porphyry bodies and rhyolitic domes crosscut the stratigraphy. The upper volcanic sequence is separated into two packages by an angular unconformity. Mineralization produced an early Pb–Zn-mineralized hydrothermal fault breccia, followed by Cu–Ag veins and late Au veins. The Pb–Zn mineralized breccia is hosted by ~30 Ma Oligocene volcanic units that form the basal sequence. The Cu–Ag and Au-rich veins overlap and crosscut the early hydrothermal features and cut the late Oligocene volcanic cover that unconformably overlie the basal sequence. Our results highlight the importance of episodes of Oligocene magmatism to the genesis of mineralization in the southwestern SMO specifically through a genetic link between Pb–Zn veins and intermediate Oligocene intrusive bodies, and of Ag and Au veins with late Oligocene volcanism.