cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.12772644
title: Genome-wide association study Summary statistics of Invasive melanoma vs controls, In situ Melanoma vs controls and In situ vs invasive melanoma (case-case)

description: Genome-wide association study Summary statistics of Invasive melanoma vs controls, In situ Melanoma vs controls and In situ vs invasive melanoma (case-case). The first GWAS meta-analysis combines GWAS summary statistics of invasive melanoma from UK Biobank (as of August 2022), FinnGen release 9, QSkin Sun and Health Study and The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA) study.

The second GWAS meta-analysis combines GWAS summary statistics of in situ melanoma from UK Biobank (as of August 2022), FinnGen release 9, QSkin Sun and Health Study and The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA) study.

The third GWAS meta-analysis combines GWAS summary statistics of in situ vs invasive (case-case; in situ code 0, invasive code 1) melanoma from UK Biobank (as of August 2022), QSkin Sun and Health Study and The Queensland Study of Melanoma: environmental and genetic associations (Q-MEGA) study.

Columns

CHR Chromosome

SNP rsid

POS Base position HG Build 37

A1 effect allele

A2 Non-effect allele

A1FREQ Allele frequency of effect allele

BETA effect estimate of effect allele

SE standard error of effect estimate

PVAL two-tailed p value

DIRECTION the Direction of effect of the SNP in each cohort ( in the order UKBB, FINNGEN, QSKIN, QMEGA 610k, QMEGA OMNI)

N sample size

See
DOI: 10.5281/zenodo.12775172
title: GCK variants and their annotations for "Underestimated risk of secondary complications in pathogenic and glucose-elevating GCK variant carriers with type 2 diabetes"

description: This file provides annoatations for GCK variants as dsecribed in "Underestimated risk of secondary complications in pathogenic and glucose-elevating GCK variant carriers with type 2 diabetes"
DOI: 10.5281/zenodo.10251252
title: Nucleotide sequence database of Copper-containing membrane monooxygenases genes for analysing primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia oxidising Nitrospira

description: Nucleotide sequences of 487 Cu-mmo genes, including amoA comammox clade A and clade B, amoA ammonia oxidizing bacteria as well as other Cu-mmo genes.
DOI: 10.5281/zenodo.11397464
title: Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing

description: Abstract:  The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.

This data sets contains:

Tab. S1 - Significant genes results

Tab. S2 - Enriched pathways_GO_Biological Processes

Tab. S3 - Enriched pathways_GO_Cellular Components

Tab. S4 - Enriched pathways_GO_Molecular Function

Tab. S5 - Enriched pathways_KEGG

Tab. S6 - EnrichEnriched pathways_Panther

Tab. S7 - Enriched pathways_Reactome

Tab. S8 - Gene counts

Tab. S9 - Gene selection for targeted analysis
DOI: 10.5281/zenodo.10700885
title: Meterological and stable carbon, oxygen and clumped isotope data of land snails Clausilia pumila, Succinella oblonga and Trochulus hispidus from Europe

description: These data include site information and collection dates of land snails (Clausilia pumila, Succinella oblonga and Trochulus hispidus), meteorological data of collection sites of molluscs derived using the ClimateEU software, as well as carbon, oxygen and clumped isotope compositions of snail shells of the mentioned three species from culturing experiments and natural populations across Europe. During the laboratory experiments individuals of the three species were kept at 12, 18 and 24 Celsius temperatures in climate chambers, fed exclusively by fresh lettuce and humidity was controlled using tap water (d18O: -9.29+-0.52 permil, V-SMOW). d13C, 18O and D47 values of snail shells from lab experiments and field-collections were determined in two laboratories (Isnt. for Nuclear Research, Debrecen, and Geological Institute, ETH Zürich) using IRMS. Detailed analysis and interpretations of the results obtained can be read in the original publication.
DOI: 10.5281/zenodo.11572831
title: Past and future effects of climate on the metapopulation dynamics of a NorthEast Atlantic seabird across two centuries

description: Datasets required to run code for contribution:

Past and future effects of climate on the metapopulation dynamics of a NorthEast Atlantic seabird across two centuries

Jana WE Jeglinski, Holly I Niven, Sarah Wanless, Robert T. Barrett, Mike P. Harris, Jochen Dierschke and Jason Matthiopoulos

Extension of a Bayesian metapopulation model fit to colony census data for all Northeast Atlantic colonies of the Northern gannet (Morus bassanus) described in Jeglinski et al. (2023) to investigate mechanistic relationships with climate and forecast metapopulation dynamics under two climate scenarios.
DOI: 10.5281/zenodo.11575618
title: Past and future effects of climate on the metapopulation dynamics of a NorthEast Atlantic seabird across two centuries

description: Datasets required to run code for contribution:

Past and future effects of climate on the metapopulation dynamics of a NorthEast Atlantic seabird across two centuries

Jana WE Jeglinski, Holly I Niven, Sarah Wanless, Robert T. Barrett, Mike P. Harris, Jochen Dierschke and Jason Matthiopoulos

Extension of a Bayesian metapopulation model fit to colony census data for all Northeast Atlantic colonies of the Northern gannet (Morus bassanus) described in Jeglinski et al. (2023) to investigate mechanistic relationships with climate and forecast metapopulation dynamics under two climate scenarios.
DOI: 10.5281/zenodo.11081564
title: Data from 'The rise of dietary diversity in coral reef fishes'
DOI: 10.5281/zenodo.10717009
title: Data supporting "Prospective impacts of windstorm risk on carbon sinks and the forestry sector: 1 an integrated assessment with Monte-Carlo simulations"

description: Simulation results for the article "Prospective impacts of windstorm risk on carbon sinks and the forestry sector: 1 an integrated assessment with Monte-Carlo simulations"
DOI: 10.5281/zenodo.8320025
title: Dataset for "Cover crop inclusion and residue retention improves soybean production and physiology in drought conditions"

description: Data and code for "Cover crop inclusion and residue retention improves soybean production and physiology in drought conditions"


CONTEXT: Soybean (Glycine max (L.) Merr.) planting has increased in central and western North Dakota despite frequent drought occurrences that limit productivity.  Soybean plants need high photosynthetic and transpiration rates to be productive, but they also need high water use efficiency when water is limited. Retaining crop residues and including cover crops in crop rotations are management strategies that could improve soybean drought resilience in the northern Great Plains.   


OBJECTIVE: We aimed to examine how a management practice that included cover crops and residue retention impacts agronomic, ecosystem water and carbon dioxide flux, and canopy-scale physiological attributes of soybeans in the northern Great Plains under drought conditions.  


METHODS:  We compared two soybean fields over two years with business-as-usual and aspirational management that included residue retention and cover crops during a drought year.  This comparison was based on yield, aboveground biomass, Phenocam images, and fluxes from eddy covariance and ancillary measurements.  These measurements were used to derive meteorological, physical, and physiological attributes with the ‘big leaf’ framework. 


RESULTS: Soybean yields were 29% higher under drought conditions in the field managed in a system that included cover crops and residue retention. This yield increase was caused by extending the maturity phenophase by 5 days, increasing agronomic and intrinsic water use efficiency by 27% and 33%, respectively, increasing water uptake, and increasing the rubisco-limited photosynthetic capacity (Vcmax25) by 42%.


CONCLUSIONS: The inclusion of cover crops and residue retention into a cropping system improved soybean productivity because of differences in water use, phenology timing, and photosynthetic capacity.


IMPLICATIONS: These results suggest that farmers can improve soybean productivity and yield stability by incorporating cover crops and residue retention into their management practices because these practices allow soybean plants to shift to a more aggressive water uptake strategy.


Code:


1_phenocam.rmd:  Code to download Phenocam data and identify phenophase transition dates.


2_Daily_CO2_Water_Fluxes.Rmd: Code to analyze daily carbon and water fluxes (Figure 1, 2 3 and Table 2).


3_Inferring_LAI_and_Height.Rmd: Code to calculate the predicted LAI and height for each day.  The output is used in the big-leaf framework.


4_Big_Leaf.Rmd: Code for the big-leaf ecophysiology estimates (Figure 4, 5 and 6; Table 3 and 4).


4_Data_Dictionary_Vairables: Code to identify the data dictionary variables.
DOI: 10.5281/zenodo.8335085
title: Dataset for "Cover crop inclusion and residue retention improves soybean production and physiology in drought conditions"

description: Data and code for "Cover crop inclusion and residue retention improves soybean production and physiology in drought conditions"


CONTEXT: Soybean (Glycine max (L.) Merr.) planting has increased in central and western North Dakota despite frequent drought occurrences that limit productivity.  Soybean plants need high photosynthetic and transpiration rates to be productive, but they also need high water use efficiency when water is limited. Retaining crop residues and including cover crops in crop rotations are management strategies that could improve soybean drought resilience in the northern Great Plains.   


OBJECTIVE: We aimed to examine how a management practice that included cover crops and residue retention impacts agronomic, ecosystem water and carbon dioxide flux, and canopy-scale physiological attributes of soybeans in the northern Great Plains under drought conditions.  


METHODS:  We compared two soybean fields over two years with business-as-usual and aspirational management that included residue retention and cover crops during a drought year.  This comparison was based on yield, aboveground biomass, Phenocam images, and fluxes from eddy covariance and ancillary measurements.  These measurements were used to derive meteorological, physical, and physiological attributes with the ‘big leaf’ framework. 


RESULTS: Soybean yields were 29% higher under drought conditions in the field managed in a system that included cover crops and residue retention. This yield increase was caused by extending the maturity phenophase by 5 days, increasing agronomic and intrinsic water use efficiency by 27% and 33%, respectively, increasing water uptake, and increasing the rubisco-limited photosynthetic capacity (Vcmax25) by 42%.


CONCLUSIONS: The inclusion of cover crops and residue retention into a cropping system improved soybean productivity because of differences in water use, phenology timing, and photosynthetic capacity.


IMPLICATIONS: These results suggest that farmers can improve soybean productivity and yield stability by incorporating cover crops and residue retention into their management practices because these practices allow soybean plants to shift to a more aggressive water uptake strategy.


Code:


1_phenocam.rmd:  Code to download Phenocam data and identify phenophase transition dates.


2_Daily_CO2_Water_Fluxes.Rmd: Code to analyze daily carbon and water fluxes (Figure 1, 2 3 and Table 2).


3_Inferring_LAI_and_Height.Rmd: Code to calculate the predicted LAI and height for each day.  The output is used in the big-leaf framework.


4_Big_Leaf.Rmd: Code for the big-leaf ecophysiology estimates (Figure 4, 5 and 6; Table 3 and 4).


4_Data_Dictionary_Vairables: Code to identify the data dictionary variables.
DOI: 10.5281/zenodo.12720307
title: Research data supporting the publication "Hierarchy of Topological Transitions in a Network Liquid"

description: This dataset contains the data used to produce each of the figures in the manuscript "Hierarchy of Topological Transitions in a Network Liquid" published in PNAS. The dataset includes configuration files for the dendrimer system generated via NPT Monte Carlo simulations and the topological analysis of the networks formed by the dendrimer particles.
DOI: 10.5281/zenodo.11245095
title: Pediatric solid tumor and lymphoma nanopore gene expression profiles
DOI: 10.5281/zenodo.12721053
title: An unambiguous POS tagging set

description: This data set contains 1,123 short, POS-tagged sentences (extracted from an earlier data set; see https://zenodo.org/records/7694423), using the Universal tag set. The sentences can easily be POS tagged by a human tagger. However, standard POS taggers struggle with these sentences. The data file contains a header row that describes each column. The first column indicates the type of sentence (either a transcript of spoken text (0) or a sentence originating from written text (1)), the second column contains the actual sentence, with ground truth POS tags. The third column indicates the index of the mistagged token, and the remaining five columns show the tags assigned (of which at least one is a mistagging) of five different taggers.
DOI: 10.5281/zenodo.11951268
title: Dataset, R code and metadata for Lim et al., Pattern matters in the aposematic colouration of Papilio polytes butterflies

description: Dataset, R code and metadata for Lim et al., Pattern matters in the aposematic colouration of Papilio polytes butterflies.
DOI: 10.5281/zenodo.12111048
title: Achromobacter sp. M1
DOI: 10.15468/dl.sf8w5g
title: Occurrence Download

description: A dataset containing 3465 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Galearis rotundifolia (Banks ex Pursh) R.M.Bateman"
 ]
}

 The dataset includes 3465 records from 114 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111037-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.843wmp
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "TaxonKey is Teratohyla pulverata (Peters, 1873)"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111038-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jhfjs6
title: Occurrence Download

description: A dataset containing 97630 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dactylorhiza viridis (L.) R.M.Bateman, Pridgeon & M.W.Chase"
 ]
}

 The dataset includes 97630 records from 810 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111040-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2c8pxn
title: Occurrence Download

description: A dataset containing 712 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Colombia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Bothrops asper (Garman, 1883)",
 "Year 2015-2024"
 ]
}

 The dataset includes 712 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111042-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yskhje
title: Occurrence Download

description: A dataset containing 11746 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Latrodectus hesperus Chamberlin & Ivie, 1935"
 ]
}

 The dataset includes 11746 records from 38 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111041-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rjahma
title: Occurrence Download

description: A dataset containing 5428 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Platanthera orbiculata (Pursh) Lindl."
 ]
}

 The dataset includes 5428 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111043-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7jphth
title: Occurrence Download

description: A dataset containing 8683 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Panthera onca (Linnaeus, 1758)"
 ]
}

 The dataset includes 8683 records from 272 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111044-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.zrm59w
title: Occurrence Download

description: A dataset containing 23270 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Latrodectus geometricus C.L.Koch, 1841, Latrodectus hesperus Chamberlin & Ivie, 1935)"
 ]
}

 The dataset includes 23270 records from 91 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111045-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gxw9mn
title: Occurrence Download

description: A dataset containing 1482766 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Psittacula krameri (Scopoli, 1769)",
 "HasCoordinate is true",
 "Year is greater than or equal to 2011",
 "Year is less than or equal to 2024"
 ]
}

 The dataset includes 1482766 records from 1115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0111039-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/whittington-ouc12217699
title: Dairy scenes, Southern Calif., 1940

description: 23 photographs of dairy cows at the Dick Hofstra Dairy, their keepers, and their environment, California, 1940. "Subject: Dairy scenes." "Client: Milk Industries; Agency: Lord Thomas, Mr. Badger; Original print order: 1 ea[ch]; Size: 8x10; Finish: gl[ossy]; 4x5, 5x7, 8x10; Re-order: 14, 3, 2; Year: 1940; Job: 010-22-161" -- on envelope front. 24 original photographs [of which 23 remain] @ 2.00 Travel lab; Amount: 48.00; 60 miles transportation @ 20 cents; Amount: 12.00; 7-1/2 hours time @ 20 cents; Amount 15.00, [total] 75.00; Operator's report (Name): Joe" -- on envelope back.
DOI: 10.25582/data.2022-12.2679410/2347942
title: Data for EMSL Project 51413 from December 2022
DOI: 10.15468/dl.yobvje
title: Occurrence Download

description: A dataset containing 498152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Prunella Vieillot, 1816",
 "BasisOfRecord is Human Observation"
 ]
}

 The dataset includes 498152 records from 385 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075864-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/whit-c170-82638
title: Christmas articles, Broadway Department Store, Southern California, 1935

description: 27 photographs of Christmas articles, Southern California, 1935. "Subject: Xmas articles, 1 to 17 inc[luded], see also 8x10; Client: Broadway Hollywood; Job: 11-14-07; Year: 1935; Original print order: 1 ea[ch]; Size: Contact; Finish: gl[ossy]; Mount: no margin" -- on envelope front. "Photographer: Dick, Dean, and Joe; Original photographs- Size: 37 to size, 2.50, 74, 18.50, 92.50; Amount: $117.50; Extra Charges: Peterson" -- on envelope back.
DOI: 10.25582/data.2021-10.2364035/2347943
title: Data for EMSL Project 51413 from October 2021
DOI: 10.15468/dl.d9jmq2
title: Occurrence Download

description: A dataset containing 223191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dendrocygna javanica (Horsfield, 1821)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 223191 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006786-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.numnn2
title: Occurrence Download

description: A dataset containing 223191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dendrocygna javanica (Horsfield, 1821)",
 "HasCoordinate is true",
 "Year is greater than or equal to 1970",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 223191 records from 29 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006784-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/whit-c170-82641
title: Christmas articles, Broadway Department Store, Southern California, 1935

description: 27 photographs of Christmas articles, Southern California, 1935. "Subject: Xmas articles, 1 to 17 inc[luded], see also 8x10; Client: Broadway Hollywood; Job: 11-14-07; Year: 1935; Original print order: 1 ea[ch]; Size: Contact; Finish: gl[ossy]; Mount: no margin" -- on envelope front. "Photographer: Dick, Dean, and Joe; Original photographs- Size: 37 to size, 2.50, 74, 18.50, 92.50; Amount: $117.50; Extra Charges: Peterson" -- on envelope back.