cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.13982582
title: Downstream data for recombination inferrence in the barn owl (Tyto alba)

description: Downstream data for the publication "The recombination landscape of the barn owl, from families to populations". 

Use with https://github.com/topalw/Recombination_barn_owl
DOI: 10.5281/zenodo.13982583
title: Downstream data for recombination inferrence in the barn owl (Tyto alba)

description: Downstream data for the publication "The recombination landscape of the barn owl, from families to populations". 

Use with https://github.com/topalw/Recombination_barn_owl
DOI: 10.5281/zenodo.13692538
title: Interseismic Strain Rate Evolution From InSAR Prior to the 2021 Mw 7.4 Maduo Earthquake

description: This repository contains the datasets from the supporting information for the manuscript:

Rutland, C., Bie, L., Johnson, J.H., Ou, Q. & Mildon, Z.K. (2024). "Interseismic Strain Rate Evolution From InSAR Prior to the 2021 Mw 7.4 Maduo Earthquake."

Data Set S1. V E derived from InSAR data from 2015/01/28–2021/05/20.Data Set S2. σV E derived from InSAR data from 2015/01/28–2021/05/20.Data Set S3. ε̇ shear derived from InSAR data from 2015/01/28–2021/05/20.Data Set S4. V E derived from InSAR data from 2015/01/28–2017/05/17.Data Set S5. σV E derived from InSAR data from 2015/01/28–2017/05/17.Data Set S6. ε̇ shear derived from InSAR data from 2015/01/28–2017/05/17.Data Set S7. V E derived from InSAR data from 2017/05/29–2019/05/19.Data Set S8. σV E derived from InSAR data from 2017/05/29–2019/05/19.Data Set S9. ε̇ shear derived from InSAR data from 2017/05/29–2019/05/19.Data Set S10. V E derived from InSAR data from 2019/05/31–2021/05/20.Data Set S11. σV E derived from InSAR data from 2019/05/31–2021/05/20.Data Set S12. ε̇ shear derived from InSAR data from 2019/05/31–2021/05/20.
DOI: 10.5281/zenodo.10557780
title: Soil respiration processed data at Palazzelli CREA_OFA citrus farm

description: Soil respiration processed data at Palazzelli CREA_OFA citrus farm
DOI: 10.5281/zenodo.8196037
title: Soil respiration processed data at Palazzelli CREA_OFA citrus farm

description: Soil respiration processed data at Palazzelli CREA_OFA citrus farm
DOI: 10.5281/zenodo.8196038
title: Soil respiration processed data at Palazzelli CREA_OFA citrus farm

description: Soil respiration processed data at Palazzelli CREA_OFA citrus farm
DOI: 10.5281/zenodo.14628666
title: Summary Statistics: Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases

description: Exome wide gene and single variant level summary statistics associated with the Nature Communications article "Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases".

 

Gene Level Association Files

gene_level_prostate_cancer_risk.txt: gene-level summary statistics for assocation with prostate cancer risk (case Vs controls)

gene_level_prostate_cancer_severity.txt: gene-level summary statistics for assocation with prostate cancer severity (aggressive prostate cancer Vs non-aggressive prostate cancer)

gene_level_prostate_cancer_agg_ctrl.txt: gene-level summary statistics for assocation of aggressive prostate cancer Vs controls

Columns

Gene Name

Gene ENSG - Ensembl gene ID

CA_model - collapsing analysis qualifying variant model (as in Supplementary Data 1 of article)

CMH_P - meta analysis P-value

CMH_OR - meta analysis odds ratio

CMH_OR_LCI - meta analysis odds ratio lower confidence interval

CMH_OR_UCI - meta analysis odds ratio upper confidence interval 

Total Qual Cases - number of cases carrying a qualifying variant

Total Unqual Cases - number of cases not carrying a qualifying variant

Total Qual Ctrls - number of controls carrying a qualifying variant

Total Unqual Ctrls - number of controls not carrying a qualifying variant

 

Single Variant level Association File

single_variant_prostate_cancer_risk.txt - single variant level summary statistics for assocation with prostate cancer risk (case Vs controls)

Columns

chr - chromosome

pos - genomic position

effect_allele

other_allele

P - meta analysis P-value

direction - direction of effect in individual cohorts (100KGP,  MCPS, UKB_SAS,  UKB_AFR, UKB_EUR, FinnGen).
DOI: 10.5281/zenodo.14628665
title: Summary Statistics: Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases

description: Exome wide gene and single variant level summary statistics associated with the Nature Communications article "Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases".

 

Gene Level Association Files

gene_level_prostate_cancer_risk.txt: gene-level summary statistics for assocation with prostate cancer risk (case Vs controls)

gene_level_prostate_cancer_severity.txt: gene-level summary statistics for assocation with prostate cancer severity (aggressive prostate cancer Vs non-aggressive prostate cancer)

gene_level_prostate_cancer_agg_ctrl.txt: gene-level summary statistics for assocation of aggressive prostate cancer Vs controls

Columns

Gene Name

Gene ENSG - Ensembl gene ID

CA_model - collapsing analysis qualifying variant model (as in Supplementary Data 1 of article)

CMH_P - meta analysis P-value

CMH_OR - meta analysis odds ratio

CMH_OR_LCI - meta analysis odds ratio lower confidence interval

CMH_OR_UCI - meta analysis odds ratio upper confidence interval 

Total Qual Cases - number of cases carrying a qualifying variant

Total Unqual Cases - number of cases not carrying a qualifying variant

Total Qual Ctrls - number of controls carrying a qualifying variant

Total Unqual Ctrls - number of controls not carrying a qualifying variant

 

Single Variant level Association File

single_variant_prostate_cancer_risk.txt - single variant level summary statistics for assocation with prostate cancer risk (case Vs controls)

Columns

chr - chromosome

pos - genomic position

effect_allele

other_allele

P - meta analysis P-value

direction - direction of effect in individual cohorts (100KGP,  MCPS, UKB_SAS,  UKB_AFR, UKB_EUR, FinnGen).
DOI: 10.15468/dl.5h424v
title: Occurrence Download

description: A dataset containing 332 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "TaxonKey is Linepithema humile (Mayr, 1868)"
 ]
}

 The dataset includes 332 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005316-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14773276
title: Replication Package of "o3-mini vs DeepSeek-R1: Which One is Safer?"

description: This dataset collects the results obtained for testing the o3-mini LLM and DeepSeek-R1 (70B) model in terms of safety.
DOI: 10.5281/zenodo.14773277
title: Replication Package of "o3-mini vs DeepSeek-R1: Which One is Safer?"

description: This dataset collects the results obtained for testing the o3-mini LLM and DeepSeek-R1 (70B) model in terms of safety.
DOI: 10.5281/zenodo.14773554
title: Research Data Chatbot
DOI: 10.5281/zenodo.14773555
title: Research Data Chatbot
DOI: 10.15468/dl.yku8dx
title: Occurrence Download

description: A dataset containing 14975 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limulus polyphemus (Linnaeus, 1758)",
 "Year 2000-2025"
 ]
}

 The dataset includes 14975 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005317-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14772959
title: Data and code for "Surface and subsurface compound marine heatwave and biogeochemical extremes under climate change"

description: """Note that data archiving is underway. This repository does not include the final version of our scripts."""

This repository provides the data and code for the manuscript "Surface and subsurface compound marine heatwave and biogeochemical extremes under climate change".

It includes python scripts to plot the manuscript's figures, as well as all necessary input files. Upon publication a neater version of these scripts will be made publicly available. 

The netcdf input files have been processed using CDO and NCO commands.A history of all commands is available in the files description. Here, we do not provide our raw data, because of too large file sizes. For more information, please contact nlegrix@liverpool.ac.uk
DOI: 10.5281/zenodo.14772958
title: Data and code for "Surface and subsurface compound marine heatwave and biogeochemical extremes under climate change"

description: This repository provides the data and code for the manuscript "Surface and subsurface compound marine heatwave and biogeochemical extremes under climate change".

It includes python scripts to plot the manuscript's figures, as well as all necessary input files. Upon publication a neater version of these scripts will be made publicly available. 

The netcdf input files have been processed using CDO and NCO commands.A history of all commands is available in the files description. Here, we do not provide our raw data, because of too large file sizes. For more information, please contact nlegrix@liverpool.ac.uk
DOI: 10.5281/zenodo.14773535
title: Data and code for "Surface and subsurface compound marine heatwave and biogeochemical extremes under climate change"

description: This repository provides the data and code for the manuscript "Surface and subsurface compound marine heatwave and biogeochemical extremes under climate change".

It includes python scripts to plot the manuscript's figures, as well as all necessary input files. Upon publication a neater version of these scripts will be made publicly available. 

The netcdf input files have been processed using CDO and NCO commands.A history of all commands is available in the files description. Here, we do not provide our raw data, because of too large file sizes. For more information, please contact nlegrix@liverpool.ac.uk
DOI: 10.5281/zenodo.14773536
title: Automatic Classification of Software Repositories: A Systematic Mapping Study - replication package

description: This is the replication package for the paper: 



Automatic Classification of Software Repositories: A Systematic Mapping Study
DOI: 10.5281/zenodo.14773537
title: Automatic Classification of Software Repositories: A Systematic Mapping Study - replication package

description: This is the replication package for the paper: 



Automatic Classification of Software Repositories: A Systematic Mapping Study
DOI: 10.17632/m4rmvt4f3n
title: A Comprehensive Global Database of Mine Tailings Flows

description: Tailings are finely ground, often toxic mine waste rock produced from mineral ore processing that are conventionally discharged as slurries into dammed storage facilities. Given that tailings disposal is necessary insofar as mining operations continue, tailings dams are perpetually evolving structures that are raised in stages over the span of several years to decades, with some impoundments being among the most voluminous anthropogenic structures in the world. The failures of some tailings impoundments have received considerable public attention in recent years due to the catastrophic human and environmental consequences caused by mass movements, as evidenced by the 2019 Feijão disaster in Brazil (272 deaths) and numerous precedents over the past century. Developing an inventory of these mass movements - or tailings flows - is an essential step to understanding the (i) magnitude-frequency statistics, (ii) internal and external preconditioning and trigger variables, (iii) breach-outflow mechanisms and (iv) downstream inundation geometry and geomorphic processes. Moreover, constructing a global database helps establish a consistent framework for reporting various properties of tailings dam failures and ensuing mass flows. Upon reviewing over 350 historical mine waste dam failures in pre-existing secondary datasets, we have developed a comprehensive database of 63 tailings flows from 1928-2020 (while following a strict case selection criteria) with the support of compiled satellite imagery, digital elevation models (DEMs) and source literature. Using a novel runout zonation method (developed by Ghahramani et al., 2020), the satellite images and DEMs were analyzed on geographic information systems (GIS) platforms to independently estimate runout distances, inundation areas and travel path angles. Contingent upon data availability or quality, we also summarized the background information, impoundment conditions and hydro-geotechnical indices to provide site-specific context to case histories. It is anticipated that the compiled data and review will broaden the scholarly understanding of breach-runout behaviour and enhance hazard-risk assessment strategies including empirical and numerical modelling. However, the compiled data must be treated with prudence. Tailings impoundments are extremely variable depending on the locality, and site-specific conditions (internal and external) are strong controls on post-breach behaviour. Even though the presented dataset is comprehensive, large-scale statistical approaches may not satisfactorily reflect the "true" site-specific field behaviour. As such, it is recommended that this dataset be used purely as a basis for screening-level assessments, case analog comparisons and academic research. For site-specific prediction studies undertaken by practitioners, targeted field observations, laboratory investigations and numerical models are essential.
DOI: 10.15468/dl.3ad42t
title: Occurrence Download

description: A dataset containing 802 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Peru",
 "TaxonKey is Atlapetes forbesi Morrison, 1947"
 ]
}

 The dataset includes 802 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005318-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9ub3rv
title: Occurrence Download

description: A dataset containing 14975 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Limulus polyphemus (Linnaeus, 1758)",
 "Year 2000-2025"
 ]
}

 The dataset includes 14975 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005319-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17632/3dmz3jtb3w
title: RNASeq - 3D Organoids Reveal Cellular and Molecular Mechanisms of Synovial Tissue Formation 1/4
DOI: 10.34740/kaggle/dsv/10619203
title: Mahanagar Yatayat Transport Dataset
DOI: 10.15468/dl.7tcjsn
title: Occurrence Download

description: A dataset containing 1073 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is South America",
 "OccurrenceStatus is Present",
 "TaxonKey is Chrysocyon brachyurus (Illiger, 1815)"
 ]
}

 The dataset includes 1073 records from 54 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005322-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7266/n7-ccc2-s109
title: Eastern Gulf of Mexico glider deployment M66 (2016-07-29 – 2016-08-12) – tag telemetry receptions
DOI: 10.17632/rpx38hyw58
title: Proteomic dataset of membrane vesicles from clinical C. acnes isolates with different antibiotics activity

description: The dataset contains the identified proteins in the membrane vesicles from six clinical C. acnes isolates by using low PH nano-HPLC-MS/MS analysis. Among the six clinical C. acnes isolates, three were detected resistant to both clindamycin and erythromycin, with MICs of &gt;128 mg/L for clindamycin and erythromycin; the other three were sensitive to both clindamycin and erythromycin, with MICs ≤2mg/L for clindamycin and ≤0.5mg/L for erythromycin.
DOI: 10.15468/dl.cradkf
title: Occurrence Download

description: A dataset containing 23553 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Acacia mearnsii De Wild., Acacia mollissima E.Miège, Acacia decurrens var. mollis Ker Gawl., Acacia decurrens var. mollissima E.Miège, Racosperma mearnsii (De Wild.) Pedley)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 23553 records from 115 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005324-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10361833
title: Comparing the Impact of Microplastics Derived from a Biodegradable and a Conventional Plastic Mulch on Plant Performance
DOI: 10.5281/zenodo.10361834
title: Comparing the Impact of Microplastics Derived from a Biodegradable and a Conventional Plastic Mulch on Plant Performance
DOI: 10.6084/m9.figshare.28312157
title: Data Table

description: data table
DOI: 10.5281/zenodo.14756356
title: Fecal microbiota composition analysis in CDKL5 deficiency disorder mouse models

description: In this study, male CDKL5-/y (CDKL5 KO) mice and their male CDKL5+/y WT littermates were investigated.

The composition of the fecal microbiota of CDKL5 KO and WT mice was analysed at different ages. Fresh feces were collected longitudinally from the same subjects at (postnatal day) P25, P32 and P70.

We conducted our analysis on two different CDKL5 null mouse lines born and raised in two distinct animal facilities: the vivarium at the National Research Council in Pisa, Italy (Ref. Amendola et al., 2014 PMID: 24838000), and the vivarium at the Max Planck Institute for Molecular Genetics in Berlin, Germany.

Bacterial DNA was extracted using the QIAamp Powerfecal DNA kit (Qiagen, Cat. no. 12830-50), and its concentration was quantified by the Nanodrop 2000 C Spectrophotometer (ThermoFisher Scientific). 

The 16S rRNA sequencing and analysis was performed by a service offered by Institute of Applied Genomics (IGA, Udine, Italy).  

Library preparation and sequencing. Libraries were prepared by following Illumina 16S Metagenomic Sequencing Library Preparation protocol in two amplification steps: an initial 35 cycle PCR amplification using locus-specific PCR primers and a subsequent amplification that integrates relevant flow-cell binding domains and unique indices (NexteraXT Index Kit, Illumina, FC‐131‐ 1001/FC‐131‐1002).

Primer sequences used for amplification:

16S F (341F) 5’- CCTACGGGNGGCWGCAG -3’

16S R (805R) 5’- GGACTACHVGGGTATCTAATCC -3’

Libraries were sequenced on a MiSeq instrument (Illumina) in paired end 300-bp mode read length. 

We provide the raw data obtained through the 16S rRNA-sequencing experiment.

This dataset contains the following files: 242 files \"fastq.gz\": Files containing the raw sequencing data (FASTQ files) of the 16S rRNA gene profiling carried out on DNA extracted from mouse fecal samples collected longitudinally (at postnatal days (P)-25, P32 and P70) in mice originated from two vivaria: Pisa vivarium (A001) and Berlin vivarium (A002).

As sequencing configuration was performed paired-end, each fragment has two raw reads with the first read in forward orientation (R1), and the second read in reverse-complement orientation (R2). Corresponding reads from the R1 and R2 files are collectively a single paired-end read. Adapter sequences masked with MiSeq Reporter, no quality clipping was provided.

File Naming Convention (Example):

ID2381-2-P25-WT2-A001-B01_S18_L001_R1_001.fastq.gz

Explanation of the symbol in the file name:



ID2381 = Sequencing ID

2 = Serial number identifying each sequenced fragment (each fragment has two files: R1 & R2)

P25 = Postnatal day at collection (P25, P32, or P70- in this case P25)

WT2 = Genotype and individual mouse ID (WT = wild-type, KO = knockout, followed by mouse ID number)

A001 = Vivarium ID (A001 = Pisa, A002 = Berlin)

B01 = Sample batch identifier

S18_L001 = Sequencing-specific information

R1 = Read direction (R1 = forward, R2 = reverse)
DOI: 10.15468/dl.awnepy
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-0.32071 42.91636,0.06308 42.91636,0.06308 43.12812,-0.32071 43.12812,-0.32071 42.91636))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Zootoca vivipara (Lichtenstein, 1823)"
 ]
}

 The dataset includes 337 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005325-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gayt7y
title: Occurrence Download

description: A dataset containing 653 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (South America, North America)",
 "OccurrenceStatus is Present",
 "TaxonKey is Speothos venaticus (Lund, 1842)"
 ]
}

 The dataset includes 653 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005326-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14013299
title: Low Temperature Atomic Layer Deposition of Elemental Bismuth

description: This study presents the first successful demonstration of growing elemental bismuth (Bi) thin films via thermal atomic layer deposition (ALD) using Bi(NMe2)3 as the precursor and Sb(SiMe3)3 as the co-reactant. The films were deposited at a relatively low temperature of 100 °C, with a growth per cycle (GPC) of 0.31-0.34 Å/cycle. Island formation marked the initial growth stages, with surface coverage reaching around 80% after 1000 cycles and full coverage between 2000 and 2500 cycles. Morphological analysis revealed that the Bi grains expanded and became more defined as the number of ALD cycles increased. This coalescence is further supported by X-ray diffraction (XRD) patterns, which show a preferential shift in growth orientation from the (012) plane to the (003) plane as the film thickness increases. X-ray photoemission spectroscopy (XPS) confirmed the presence of metallic Bi with minimal surface oxidation. Temperature-dependent sheet resistance measurements highlight the semimetallic nature of Bi, with a room temperature resistivity of ≈200 µΩcm for the 2500 cycles Bi. Temperature-dependent sheet resistance was also associated with a transition in carrier-type dominance from electrons at higher temperatures to holes at lower temperatures.