cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.p86pxe
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Pavo muticus Linnaeus, 1766",
 "Year 1000-1980"
 ]
}

 The dataset includes 26 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071708-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13335359
title: ICSE 2025 Artifact for "An Empirical Study on Package-Level Deprecation in Python Ecosystem"

description: Artifact

This artifact includes the source code and data needed to reproduce the results of our paper.

Files





inactive_task: This folder contains the dataset we collected, including:









A list of all packages in PyPI as of 2023.1.9 in all_package.json

A list of halted packages in halted_packages.pkl

A list of packages that haven't received any commit for a long time in long_time_no_commit.json

A list of inactive packages and their corresponding GitHub repositories in inactive_pkg_repo_list.json

A mapping of packages to their corresponding GitHub links in pgk2url.json

A dataset with details in deprecation_dataset/, which includes rationales, alternative solutions, and package characteristics (RQ1). Click [here](inactive_task/deprecation_dataset/README.md) for more details.








ghd_dataset: This folder contains the dependency information for PyPI, which we used to build the dependency network. Please unzip the file before use.







down_deps: The folder contains scripts to process our data, including









similar_brothers: A script to find similar brother packages of deprecated packages.

delta_of_downdeps.py: A script that calculates the gain of downstream dependencies.



regression: This folder contains scripts for the models that estimate the effect of deprecation announcements, which can be used to reproduce the results of RQ2.

questionnaire_data: The folder includes the questionnaire prototype and responses (RQ3, 4). Click [here](./questionnaire_data/README.md) for more details.
DOI: 10.5281/zenodo.13335360
title: ICSE 2025 Artifact for "An Empirical Study on Package-Level Deprecation in Python Ecosystem"

description: Artifact

This artifact includes the source code and data needed to reproduce the results of our paper.

Files





inactive_task: This folder contains the dataset we collected, including:









A list of all packages in PyPI as of 2023.1.9 in all_package.json

A list of halted packages in halted_packages.pkl

A list of packages that haven't received any commit for a long time in long_time_no_commit.json

A list of inactive packages and their corresponding GitHub repositories in inactive_pkg_repo_list.json

A mapping of packages to their corresponding GitHub links in pgk2url.json

A dataset with details in deprecation_dataset/, which includes rationales, alternative solutions, and package characteristics (RQ1). Click [here](inactive_task/deprecation_dataset/README.md) for more details.








ghd_dataset: This folder contains the dependency information for PyPI, which we used to build the dependency network. Please unzip the file before use.







down_deps: The folder contains scripts to process our data, including









similar_brothers: A script to find similar brother packages of deprecated packages.

delta_of_downdeps.py: A script that calculates the gain of downstream dependencies.



regression: This folder contains scripts for the models that estimate the effect of deprecation announcements, which can be used to reproduce the results of RQ2.

questionnaire_data: The folder includes the questionnaire prototype and responses (RQ3, 4). Click [here](./questionnaire_data/README.md) for more details.
DOI: 10.15468/dl.9w4ahg
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((146.66494 -34.509479, 146.66494 -34.516217, 146.667186 -34.516217, 146.667186 -34.509479, 146.66494 -34.509479))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071709-240626123714530/datasets/export for details.
DOI: 10.15468/dl.g5gbsr
title: Occurrence Download

description: A dataset containing 176 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Pavo muticus Linnaeus, 1766"
 ]
}

 The dataset includes 176 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071710-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.65wasn
title: Occurrence Download

description: A dataset containing 268199 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ukraine",
 "Geometry POLYGON((13.35277 40.74421,49.64723 40.74421,49.64723 55.25579,13.35277 55.25579,13.35277 40.74421))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "Year 1626-1996"
 ]
}

 The dataset includes 268199 records from 431 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071704-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.evazsb
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((147.439741 -34.509479, 147.439741 -34.516217, 147.441987 -34.516217, 147.441987 -34.509479, 147.439741 -34.509479))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071711-240626123714530/datasets/export for details.
DOI: 10.34740/kaggle/dsv/9191562
title: Forex Exchange Rates Since 2004 (Updated Daily)
DOI: 10.15468/dl.x2dpqs
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Rhododendron ×sinosimulans D.F.Chamb."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071712-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3u2up5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "MULTIPOLYGON (((147.713728 -34.509479, 147.715974 -34.509479, 147.715974 -34.507234, 147.713728 -34.507234, 147.713728 -34.509479)), ((147.713728 -34.509479, 147.706991 -34.509479, 147.706991 -34.513971, 147.713728 -34.513971, 147.713728 -34.509479)), ((147.715974 -34.507234, 147.71822 -34.507234, 147.71822 -34.504988, 147.722712 -34.504988, 147.722712 -34.509479, 147.729449 -34.509479, 147.729449 -34.507234, 147.724957 -34.507234, 147.724957 -34.504988, 147.731695 -34.504988, 147.731695 -34.500496, 147.715974 -34.500496, 147.715974 -34.507234)), ((147.722712 -34.509479, 147.71822 -34.509479, 147.71822 -34.513971, 147.722712 -34.513971, 147.722712 -34.509479)))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071713-240626123714530/datasets/export for details.
DOI: 10.15468/dl.8qbkkc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((147.76089 -34.504988, 147.76089 -34.509479, 147.756399 -34.509479, 147.756399 -34.516217, 147.76089 -34.516217, 147.76089 -34.513971, 147.763136 -34.513971, 147.763136 -34.504988, 147.76089 -34.504988))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071714-240626123714530/datasets/export for details.
DOI: 10.5281/zenodo.10035682
title: Large grazers suppress a foundational plant and reduce soil carbon concentration in eastern US saltmarshes

description: Supporting data for the submitted manuscript currently titled "Large grazers suppress a foundational plant and reduce soil carbon in eastern US saltmarshes". "Observational data Spr.Fall 2017.xlsx" contains all data collected for eastern US grazing survey. "Cumberland experiment.xlsx" contains all data collected for grazing experiment on Cumberland Island, GA, USA. Each data workbook contains a metadata tab to help guide users.
DOI: 10.5281/zenodo.10035683
title: Large grazers suppress a foundational plant and reduce soil carbon concentration in eastern US saltmarshes

description: Supporting data for the submitted manuscript currently titled "Large grazers suppress a foundational plant and reduce soil carbon in eastern US saltmarshes". "Observational data Spr.Fall 2017.xlsx" contains all data collected for eastern US grazing survey. "Cumberland experiment.xlsx" contains all data collected for grazing experiment on Cumberland Island, GA, USA. Each data workbook contains a metadata tab to help guide users.
DOI: 10.5281/zenodo.13335333
title: Prognostic value of a modified pathological staging system for gastric cancer based on the number of retrieved lymph nodes and metastatic lymph node ratio raw data

description: Clinical data from the US Surveillance, Epidemiology, and End Results (SEER) Program from 2010-2015 (https://seer.cancer.gov/) was extracted and analyzed as training set, data from 2016-2017 was adopted as internal validation set. Data from The Cancer Genome Atlas Program (TCGA) (https://portal.gdc.cancer.gov/) and prognosis data from Gastrointestinal surgery Department, Third Affiliated Hospital of Sun Yat-sen University were applied as external validation sets. 

Screening criteria for gastric cancer cases were as follow: exclusion of cases with only autopsy or death certificate, cases where initial tumor location was not stomach, patients with stage 0 and stage IV, cases without radical surgery, non-adenocarcinoma cases, death cases within one month after operation, and cases with unknown lymph node information and AJCC TNM stage.

The study analyzed various factors such as age of diagnosis (<50 years, 50-69 years, >69 years), gender, race (white, black, other), AJCC T stage (T1-T4b), AJCC TNM stage (I-III), primary tumor location (stomach body, antrum/pylorus, cardia/fundus, greater gastric recurve, lesser gastric recurve, overlapping area, NOS), Clinical features such as tumor size (≥5cm,<5cm, unknown), tumor grade (I-IV), chemotherapy, radiotherapy, number of lymph nodes retrieved and number of metastases, and lymph node positive rate. The populations of American Indian/Alaskan and Asian/Pacific Islander were classified as "other" due to small sample sizes. Tumor grade was also analyzed, with grades I-IV representing highly differentiated, moderately differentiated, poorly differentiated, and signed-ring cell carcinoma, respectively. Overall survival (OS) is the time from cancer diagnosis to death from any cause, while disease-specific survival (DSS) is the time from cancer diagnosis to death specifically due to the disease.
DOI: 10.5281/zenodo.13335334
title: Prognostic value of a modified pathological staging system for gastric cancer based on the number of retrieved lymph nodes and metastatic lymph node ratio raw data

description: Clinical data from the US Surveillance, Epidemiology, and End Results (SEER) Program from 2010-2015 (https://seer.cancer.gov/) was extracted and analyzed as training set, data from 2016-2017 was adopted as internal validation set. Data from The Cancer Genome Atlas Program (TCGA) (https://portal.gdc.cancer.gov/) and prognosis data from Gastrointestinal surgery Department, Third Affiliated Hospital of Sun Yat-sen University were applied as external validation sets. 

Screening criteria for gastric cancer cases were as follow: exclusion of cases with only autopsy or death certificate, cases where initial tumor location was not stomach, patients with stage 0 and stage IV, cases without radical surgery, non-adenocarcinoma cases, death cases within one month after operation, and cases with unknown lymph node information and AJCC TNM stage.

The study analyzed various factors such as age of diagnosis (<50 years, 50-69 years, >69 years), gender, race (white, black, other), AJCC T stage (T1-T4b), AJCC TNM stage (I-III), primary tumor location (stomach body, antrum/pylorus, cardia/fundus, greater gastric recurve, lesser gastric recurve, overlapping area, NOS), Clinical features such as tumor size (≥5cm,<5cm, unknown), tumor grade (I-IV), chemotherapy, radiotherapy, number of lymph nodes retrieved and number of metastases, and lymph node positive rate. The populations of American Indian/Alaskan and Asian/Pacific Islander were classified as "other" due to small sample sizes. Tumor grade was also analyzed, with grades I-IV representing highly differentiated, moderately differentiated, poorly differentiated, and signed-ring cell carcinoma, respectively. Overall survival (OS) is the time from cancer diagnosis to death from any cause, while disease-specific survival (DSS) is the time from cancer diagnosis to death specifically due to the disease.
DOI: 10.15468/dl.zav8jt
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.162888 -34.509479, 148.162888 -34.513971, 148.160642 -34.513971, 148.160642 -34.516217, 148.174117 -34.516217, 148.174117 -34.513971, 148.176363 -34.513971, 148.176363 -34.511725, 148.171871 -34.511725, 148.171871 -34.509479, 148.169626 -34.509479, 148.169626 -34.513971, 148.16738 -34.513971, 148.16738 -34.509479, 148.162888 -34.509479))"
 ]
}

 The dataset includes 37 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071715-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.13335608
title: Food Choice Motives of Guardians of Trilok Academy Kathmandu with reference to Gender
DOI: 10.5281/zenodo.13335609
title: Food Choice Motives of Guardians of Trilok Academy Kathmandu with reference to Gender
DOI: 10.5281/zenodo.12732116
title: Data for the publication "MgB2Se4 Spinels (B = Sc, Y, Er, Tm) as Potential Mg-Ion Solid Electrolytes – Partial Ionic Conductivity and the Ion Migration Barrier"

description: Description Datasets

Datasets are obtained from X-ray diffraction (XRD), Rietveld analysis, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, electrochemical impedance spectroscopy (EIS), chronoamperometry (CA), chronopotentiometry (CP) and linear sweep voltammetry (LSV).

Abstract

The magnesium chalcogenide spinel MgSc~2~Se~4~ with high Mg-ion room-temperature conductivity has recently attracted interest as solid electrolyte for magnesium ion batteries. Its ionic/electronic mixed-conducting nature and the influence of the spinel composition on the conductivity and Mg^2+^ migration barrier are yet not well understood. Here, results from a combined experimental and computational study on four MgB~2~Se~4~ spinels (B = Sc, Y, Er, Tm) are presented. The room-temperature ionic conductivities (σ~ion~ = 2x10^–5^–7x10^–5^ S cm^–1^) of the spinels are accurately measured, as electron transport is effectively suppressed by purely Mg-ion conducting electrode interlayers. Using the same approach, reversible Mg plating/stripping as well as good electrochemical stability are achieved. Driven by the good accordance of the computationally and experimentally obtained Mg^2+^ migration barriers E~a~(th) and E~a~, respectively, further periodic density functional calculations are performed on the MgB~2~Se~4~ spinel system, revealing the role of trigonal distortion on the migration path geometry and E~a~(th). These findings provide deeper understanding how to reach small Mg^2+^ migration barriers E~a~ in the MgB~2~Se~4~ spinels.
DOI: 10.5281/zenodo.12732117
title: Data for the publication "MgB2Se4 Spinels (B = Sc, Y, Er, Tm) as Potential Mg-Ion Solid Electrolytes – Partial Ionic Conductivity and the Ion Migration Barrier"

description: Description Datasets

Datasets are obtained from X-ray diffraction (XRD), Rietveld analysis, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, electrochemical impedance spectroscopy (EIS), chronoamperometry (CA), chronopotentiometry (CP) and linear sweep voltammetry (LSV).

Abstract

The magnesium chalcogenide spinel MgSc~2~Se~4~ with high Mg-ion room-temperature conductivity has recently attracted interest as solid electrolyte for magnesium ion batteries. Its ionic/electronic mixed-conducting nature and the influence of the spinel composition on the conductivity and Mg^2+^ migration barrier are yet not well understood. Here, results from a combined experimental and computational study on four MgB~2~Se~4~ spinels (B = Sc, Y, Er, Tm) are presented. The room-temperature ionic conductivities (σ~ion~ = 2x10^–5^–7x10^–5^ S cm^–1^) of the spinels are accurately measured, as electron transport is effectively suppressed by purely Mg-ion conducting electrode interlayers. Using the same approach, reversible Mg plating/stripping as well as good electrochemical stability are achieved. Driven by the good accordance of the computationally and experimentally obtained Mg^2+^ migration barriers E~a~(th) and E~a~, respectively, further periodic density functional calculations are performed on the MgB~2~Se~4~ spinel system, revealing the role of trigonal distortion on the migration path geometry and E~a~(th). These findings provide deeper understanding how to reach small Mg^2+^ migration barriers E~a~ in the MgB~2~Se~4~ spinels.
DOI: 10.5281/zenodo.13335560
title: Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding

description: Raw Illumina MiSeq data in zipped FASTQ format related to the manuscript "Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding" (DOI: https://doi.org/10.1016/j.foodres.2024.114901).

Lorusso, L., Shum, P., Piredda, R., Mottola, A., Maiello, G., Cartledge, E. L., Neave E. F., & Di Pinto A., Mariani, S. (2024). Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding. Food Research International, https://doi.org/10.1016/j.foodres.2024.114901.
description: In the global processed seafood industry, disparate actors play different roles along the supply chain, creating multiple opportunities for mistakes, malpractice, and fraud. As a consequence, consumers may be exposed to non-authentic products, which hinder informed purchasing decisions and broader efforts to improve trade transparency and sustainability. Here, we characterised the taxonomic composition of 62 processed seafood products in Italian, British and Albanian retailers, purposefully obtained from different supply routes, using multiple DNA metabarcoding markers. By combining molecular results with metadata reported on labels, we revealed patterns of mislabelling in 24 products (39%) across sampling regions, denoting lack of transparency of processed seafood products based on resources sourced from either Europe or globally. We show that the accuracy of label claims and the mis-represented and underestimated levels of traded biodiversity are largely determined by the management of raw material by global processors. Our study shows that DNA metabarcoding is a powerful and novel authentication tool that is mature for application at different stages of the seafood supply chain to protect consumers and improve the sustainable management of fish stocks.
DOI: 10.5281/zenodo.13335561
title: Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding

description: Raw Illumina MiSeq data in zipped FASTQ format related to the manuscript "Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding" (DOI: https://doi.org/10.1016/j.foodres.2024.114901).

Lorusso, L., Shum, P., Piredda, R., Mottola, A., Maiello, G., Cartledge, E. L., Neave E. F., & Di Pinto A., Mariani, S. (2024). Mismanagement and poor transparency in the European processed seafood supply revealed by DNA metabarcoding. Food Research International, https://doi.org/10.1016/j.foodres.2024.114901.
description: In the global processed seafood industry, disparate actors play different roles along the supply chain, creating multiple opportunities for mistakes, malpractice, and fraud. As a consequence, consumers may be exposed to non-authentic products, which hinder informed purchasing decisions and broader efforts to improve trade transparency and sustainability. Here, we characterised the taxonomic composition of 62 processed seafood products in Italian, British and Albanian retailers, purposefully obtained from different supply routes, using multiple DNA metabarcoding markers. By combining molecular results with metadata reported on labels, we revealed patterns of mislabelling in 24 products (39%) across sampling regions, denoting lack of transparency of processed seafood products based on resources sourced from either Europe or globally. We show that the accuracy of label claims and the mis-represented and underestimated levels of traded biodiversity are largely determined by the management of raw material by global processors. Our study shows that DNA metabarcoding is a powerful and novel authentication tool that is mature for application at different stages of the seafood supply chain to protect consumers and improve the sustainable management of fish stocks.
DOI: 10.5281/zenodo.11469859
title: NLINV-Net Pretrained Network Weights and Example Reconstructions
DOI: 10.5281/zenodo.10845041
title: NLINV-Net Pretrained Network Weights and Example Reconstructions
DOI: 10.5281/zenodo.10493120
title: NLINV-Net Pretrained Network Weights and Example Reconstructions
DOI: 10.5281/zenodo.10493121
title: NLINV-Net Pretrained Network Weights and Example Reconstructions
DOI: 10.15468/dl.z2g728
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((148.225771 -34.509479, 148.225771 -34.511725, 148.230262 -34.511725, 148.230262 -34.509479, 148.225771 -34.509479))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071717-240626123714530/datasets/export for details.
DOI: 10.15468/dl.6b3t28
title: Occurrence Download

description: A dataset containing 917 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Donus ovalis Skuhrovec, 2008"
 ]
}

 The dataset includes 917 records from 26 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071718-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.11467965
title: Pan-cancer atlas of endothelial cells

description: Datasets used to generate a pan-cancer atlas of endothelial cells and additional datasets generated with sorted endothelial cells used for validation.
DOI: 10.5281/zenodo.11467966
title: Pan-cancer atlas of endothelial cells

description: Datasets used to generate a pan-cancer atlas of endothelial cells and additional datasets generated with sorted endothelial cells used for validation.