cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28616111.v1
title: 21District-M&F-1990.xlsx

description: This study investigates the global epidemiological burden of lower respiratory infections (LRI) attributable to <i>Klebsiella pneumoniae</i> from 1990 to 2021, using data from the Global Burden of Disease Study (GBD) 2021. The findings reveal that globally, disability-adjusted life years (DALYs) from <i>Klebsiella pneumoniae</i>-associated LRI decreased from 16,701,044 (95% UI: 14,220,055 to 19,183,469) in 1990 to 6,935,440 (95% UI: 5,953,328 to 8,007,786) in 2021, while deaths declined from 239,367 (95% UI: 212,553 to 268,072) to 175,783 (95% UI: 158,749 to 193,924). The age-standardized DALYs rate dropped from 313.1 (95% UI: 266.6 to 359.7) to 87.9 (95% UI: 75.4 to 101.5), and the death rate decreased from 4.5 (95% UI: 4.0 to 5.0) to 2.2 (95% UI: 2.0 to 2.5). In 2021, the highest rates were observed in Oceania and Sub-Saharan Africa, particularly in Central African Republic, Niger, and Zimbabwe, while the lowest rates were found in Australasia, High-income North America, Eastern Europe, and East Asia, especially in the UAE, Australia, and Qatar. Higher rates were noted among both males and females under 10 and over 65 years old. Although most regions experienced decreases in age-standardized rates from 1990 to 2021, Southern Latin America exhibited an increase. Additionally, age-standardized DALYs and death rates generally declined with increasing socio-demographic index (SDI). The global burden of LRI due to <i>Klebsiella pneumoniae</i> significantly decreased over the study period, but lower SDI regions, children, and the elderly remain vulnerable and require targeted interventions to further reduce this burden.
DOI: 10.15468/dl.3gwq4q
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Xanthomonas vasicola Vauterin et al., 1995"
 ]
}

 The dataset includes 148 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014955-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8mut52
title: Occurrence Download

description: A dataset containing 15027 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachyramphus viridis (Vieillot, 1816)"
 ]
}

 The dataset includes 15027 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014954-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7qh9at
title: Occurrence Download

description: A dataset containing 26 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Monolexis fuscicornis Forster, 1862",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 26 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014957-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3b58rq
title: Occurrence Download

description: A dataset containing 30373 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachyramphus castaneus (Jardine & Selby, 1827)"
 ]
}

 The dataset includes 30373 records from 69 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014956-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.12761121
title: Cryo-EM structure refinement for group II intron ribozyme

description: This dataset contains the trajectories obtained performing metainference ensemble refinement of the PDB structure 6ME0, a Group II Intron ribozyme. Also restraints on the secondary structure were kept for the first part of the trajectories. 

The refinement has been done with different replica frameworks: 8, 16, 32 and 64 replicas. All these sets of simulations are independent from each other. Each replica shows only the second part of the trajectory (5 ns), after the removal of the restraints on the secondary structure. 

The trajectories are without solvent/ions and are divided in multiple files. 

1-plain-md contains a plain MD simulation of 1 microsecond of the same system, without any refinement.

Input files can be found at https://github.com/ElisPo/Cryo-EM-refinement/
DOI: 10.5281/zenodo.12761120
title: Cryo-EM structure refinement for group II intron ribozyme

description: This dataset contains the trajectories obtained performing metainference ensemble refinement of the PDB structure 6ME0, a Group II Intron ribozyme. Also restraints on the secondary structure were kept for the first part of the trajectories. 

The refinement has been done with different replica frameworks: 8, 16, 32 and 64 replicas. All these sets of simulations are independent from each other. Each replica shows only the second part of the trajectory (5 ns), after the removal of the restraints on the secondary structure. 

In the files NA-ref and desres-ref, are the trajectories for control simulations, performed with 16 replicas, changing ions in solution from K to NA (NA-ref), and changing RNA force field from OL3 to desres (dedres-ref). There are 10 ns per replica, the first 5 ns have restraints on the helices, while the last 5 ns are only with metainference refinement. Also topologies for these two setups are present.

The trajectories are without solvent/ions and are divided in multiple files. 

1-plain-md contains a plain MD simulation of 1 microsecond of the same system, without any refinement.

2-plain-md contains the continuation of this trajectory, for 1 more microsecond.

Input files can be found at https://github.com/ElisPo/Cryo-EM-refinement/
DOI: 10.5281/zenodo.15039869
title: Cryo-EM structure refinement for group II intron ribozyme

description: This dataset contains the trajectories obtained performing metainference ensemble refinement of the PDB structure 6ME0, a Group II Intron ribozyme. Also restraints on the secondary structure were kept for the first part of the trajectories. 

The refinement has been done with different replica frameworks: 8, 16, 32 and 64 replicas. All these sets of simulations are independent from each other. Each replica shows only the second part of the trajectory (5 ns), after the removal of the restraints on the secondary structure. 

In the files NA-ref and desres-ref, are the trajectories for control simulations, performed with 16 replicas, changing ions in solution from K to NA (NA-ref), and changing RNA force field from OL3 to desres (dedres-ref). There are 10 ns per replica, the first 5 ns have restraints on the helices, while the last 5 ns are only with metainference refinement. Also topologies for these two setups are present.

The trajectories are without solvent/ions and are divided in multiple files. 

1-plain-md contains a plain MD simulation of 1 microsecond of the same system, without any refinement.

2-plain-md contains the continuation of this trajectory, for 1 more microsecond.

Input files can be found at https://github.com/ElisPo/Cryo-EM-refinement/
DOI: 10.15468/dl.pj8yre
title: Occurrence Download

description: A dataset containing 3472 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Commelina Plum. ex L.",
 "Year 1000-1900"
 ]
}

 The dataset includes 3472 records from 136 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014958-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57745/0sh5jm
title: Liste_molecules_organiques_BAPPOP.tab

description: :unav
DOI: 10.57745/3lhlba
title: BAPPOP_jeu_de_donnees.tab

description: :unav
DOI: 10.57745/clfclm
title: Organic_molecules_list_BAPPOP.tab

description: :unav
DOI: 10.57745/duhonv
title: Readme.txt

description: :unav
DOI: 10.57745/fte0j0
title: BAPPOP_dataset.tab

description: :unav
DOI: 10.57745/jjuqcb
title: Dictionary_BAPPOP.tab

description: :unav
DOI: 10.57745/nqxape
title: Plant_species_list_BAPPOP.tab

description: :unav
DOI: 10.57745/rwibki
title: Liste_especes_vegetales_BAPPOP.tab

description: :unav
DOI: 10.57745/ubshay
title: Read_me_BAPPOP.csv

description: :unav
DOI: 10.57745/wsrtgs
title: Dictionnaire_BAPPOP.tab

description: :unav
DOI: 10.5066/p9r1xbpg
title: Airborne electromagnetic and magnetic survey data, southwestern San Joaquin Valley near Maricopa, California, 2018

description: Airborne electromagnetic (AEM) and magnetic survey data were collected during November 2018 over a total distance of 1,480 line kilometers in the Maricopa Flats and surrounding areas of southwestern San Joaquin Valley of California adjacent to the Buena Vista, Midway Sunset, Yowlumne, Los Lobos, Pioneer, Landslide, San Emidio Nose, Rio Viejo, and White Wolf oil fields. These data were collected in support of groundwater salinity mapping and hydrogeologic framework development as part of the U.S. Geological Survey California Oil, Gas, and Groundwater program and the California State Water Resources Control Board’s Oil and Gas Regional Monitoring Program. Data were acquired by SkyTEM ApS with the SkyTEM 312 time-domain helicopter-borne electromagnetic system together with a Geometrics G822A cesium vapor magnetometer. The survey was flown at a nominal flight height of 35 m above terrain along block-style lines with a nominal spacing of 300 m. The AEM typical maximum depth of investigation is between 150 and 300 m. This data release includes minimally processed (raw) AEM and raw/processed magnetic data, fully processed AEM data used for resistivity model development, and laterally constrained inverted resistivity models. The complete data package received from the contractor is included in separate zip-file directory and described in the contractor's report.
DOI: 10.5281/zenodo.15030238
title: When Tools Overlook Domain Knowledge: An Empirical Study of Refactoring in Scientific Software

description: Abstract

Refactoring is a critical process for improving code quality, but anecdotal evidence has shown that refactoring in scientific software (Sci-SW ) is not always feasible. The inherently exploratory nature of Sci-OSS development, characterized by evolving requirements and limited adoption of traditional software engineering practices, could present significant challenges to refactoring. However, there is no systematic study exploring refactoring practices in Sci-OSS. To bridge this gap, we explore the effectiveness of three state-of-the-art refactoring detection tools: RefDiff (C), RefactoringMiner (Java), and PyRef (Python) to detect refactorings in scientific open-source software (Sci-OSS). Our findings reveal that these tools have significant limitations, detecting fewer refactorings in Sci-OSS than non-scientific OSS (Non-Sci-OSS). Through a mixed-method approach, we identified seven new types of refactorings in Sci-OSS, with 67.54% of undetected refactorings requiring domain knowledge. To complement our analysis of the refactoring code changes, we conducted surveys with 47 practitioners experienced in refactoring Sci-OSS and 14 follow-up interviews to gain deeper insights into the associated challenges. Our results revealed seven novel challenges for Sci-OSS-refactoring, including a domain knowledge gap. These findings emphasize the necessity for specialized tools and strategies to support refactoring in Sci-OSS effectively

Replication instructions

The project is written in Python 3.12.0

The requirements file contains all the necessary packages to run the project.To install the required packages, run the following command:



pip install -r requirements.txt


Once the required packages are installed, 

To download refactoring data from GitHub, 



    1. Add your GitHub API token in RQ1/scripts/mysettings.py    2. Run the download_data_from_github.py file in the RQ1/scripts folder.


This should download all the required files necessary to the data folder from GitHub

Once you have all the data, then install the refactoring detection tools:The installation instructions are listed below:



    - For PyRef: https://github.com/PyRef/PyRef    - For RefactoringMiner3.0: https://github.com/tsantalis/RefactoringMiner    - For RefDiff2.0: https://github.com/aserg-ufmg/RefDiff


Once you have the refactoring detection tools installed. Please change the execution path in the respective file:For example, change the pyref execution path in pyref_script.py file in RQ1/scripts folder.

Once you have changed the execution paths, you should be able to run the refactoring detection tool on all the collected data.

The detection tools will create a JSON file with the list of detected refactorings for every refactoring instance with the name format as 'repo_name_issue_number'.

you can now run the scripts in the RQ1/scripts folder to replicate the results.
DOI: 10.48597/4kcz-yrgg
title: Measurement of Meteorology at SIRTA Atmospheric Research Observatory

description: Measurement of Meteorology at SIRTA Atmospheric Research Observatory
DOI: 10.48597/hua4-g7ht
title: Measurement of Meteorology at SIRTA Atmospheric Research Observatory

description: Measurement of Meteorology at SIRTA Atmospheric Research Observatory
DOI: 10.48597/nebj-gw2q
title: Meteorology at SIRTA Atmospheric Research Observatory

description: Measurement of Meteorology at SIRTA Atmospheric Research Observatory
DOI: 10.48597/stch-sfe9
title: Measurement of Meteorology at SIRTA Atmospheric Research Observatory

description: Measurement of Meteorology at SIRTA Atmospheric Research Observatory
DOI: 10.48597/wm54-y63a
title: Measurement of Meteorology at SIRTA Atmospheric Research Observatory

description: Measurement of Meteorology at SIRTA Atmospheric Research Observatory
DOI: 10.15468/dl.mqmysx
title: Occurrence Download

description: A dataset listing the 4033369 species recorded in GBIF matching the query:
{ }

 The dataset's 4033369 records were derived from 71826 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014947-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.98gyxz
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Brazil",
 "TaxonKey is Baccharis gaucha G.Heiden"
 ]
}

 The dataset includes 14 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014961-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/j0obpe
title: Raw data for "Geraniol – a plant biocidal modifier of flax fibres used in PLA-based biocomposites"

description: Raw data for PLA-based materials containing 20% flax fibers modified with 1%, 5%, and 10% geraniol. The data also includes files for neat PLA and PLA containing 20% non-modified flax fibers. The archive contains files obtained during Instron tests, DMA, DSC, TG, wettability, and biocidal activity tests.
DOI: 10.15468/dl.y6uuur
title: Occurrence Download

description: A dataset containing 9095 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachyramphus marginatus (Lichtenstein, 1823)"
 ]
}

 The dataset includes 9095 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014962-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3wdmcu
title: Occurrence Download

description: A dataset containing 22974 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachyramphus validus (Lichtenstein, 1823)"
 ]
}

 The dataset includes 22974 records from 52 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014963-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57782/otdzir
title: Replication Data for: Anthropogenic fire reduces migratory bird abundance, diversity and body mass gain at a stopover site

description: Files related to the publication "Anthropogenic fire reduces migratory bird abundance, diversity and body mass gain at a stopover site". Included are R scripts used to model effects of fire on number of birds and species diversity as well as to model fire effects on stopover duration and changes in body mass, fat and muscle scores of indviduals recaptured. Furthermore, original data on all individuals captured and re-captured within the study are provided.
DOI: 10.57782/otdzir/9x1nt4
title: Fire amur final recapture models.R

description: R script used to model effects of fire on bird stopover decision and individual changes in body mass, fat and muscle scores.
DOI: 10.57782/otdzir/izvwro
title: MuraviovkaPark_2011-2015.csv

description: Data of all birds captured at the study site within the study
DOI: 10.57782/otdzir/pqtrzu
title: Final amur fire analysis.R

description: R script used to model effects of fire on bird occurrence
DOI: 10.57782/otdzir/uja1cc
title: fire_individual_recaptures.csv

description: Data of individual recpatured within the study period
DOI: 10.15468/dl.5rggk8
title: Occurrence Download

description: A dataset containing 819 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is one of (France, Italy, Tunisia, Algeria)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Brassica insularis Moris"
 ]
}

 The dataset includes 819 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014965-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.57782/76hp38
title: Replication Data for: Lunar cycle and moonlight intensity influence nocturnal migration patterns in a small songbird

description: Data and R scripts related to the publication "Lunar cycle and moonlight intensity influence nocturnal migration patterns in a small songbird". The R file contains the script used to analyze and visualize the data, whereas as the csv file contains the actual data (hourly weather parameters and trapping data of Eurasian skylarks Alauda arvensis).
DOI: 10.57782/76hp38/7bbixs
title: skylark_r.csv

description: Data on hourly weather parameters and the number of skylarks captured and ringed at Münster, Germany
DOI: 10.57782/76hp38/vmntdv
title: Analysis_visualisation_moon_migration.R

description: R script used to analyze and visualize the data
DOI: 10.15468/dl.jdtvfy
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Peperomia segregata T.S.Dantas, Carv.-Silva & P.E.A.S.Câmara"
 ]
}

 The dataset includes 12 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014964-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rbu4ge
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Millidium minutissimum (Weber & Mohr, 1804)",
 "HasGeospatialIssue is false",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014966-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.18150/nt1x3z
title: Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex

description: The dataset contains three-dimensional, whole-brain density maps of neurons expressing the calcium-binding protein Calbindin (CB+) of three individuals (F, 3 years, 5 months, 309.5 g; F, 3 years, 7 months, 20 days, 441 g; M, 3 years 7 months, 21 days, 343 g) of the Common Marmoset (Callithrix jacchus) monkey.For each hemisphere, every fifth section covering the entire brain was processed with diaminobenzidine (DAB) immunohistochemistry using a monoclonal antibody (AB_10000347). Stained sections were scanned using an Aperio Scanscope AT Turbo (Leica Biosystems) at ×20 magnification. Subsequently, the density maps were computed using a combination of automated cell identification, three-dimensional reconstruction, and cytoarchitecture-aware registration.The results are provided as Neuroimaging Informatics Technology Initiative (NIfTI) datasets, spreadsheets, and Python scripts and datasets to reproduce the deep learning model for automated cell identification.
DOI: 10.15468/dl.mf327y
title: Occurrence Download

description: A dataset listing the 4639 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biodiversitätsdatenbank Nationalpark Kalkalpen"
 ]
}

 The dataset's 4639 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0014960-250310093411724/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.