cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2h0gjj
title: CCDC 2294357: Experimental Crystal Structure Determination

description: Related Article: Sebastián Chaves, Mario Macías, Rodolfo Quevedo|2023|J.Mol.Struct.|1298|137079|doi:10.1016/j.molstruc.2023.137079
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h0mnt
title: CCDC 2294516: Experimental Crystal Structure Determination

description: Related Article: Michał Sulik, Diana Fontinha, Dietmar Steverding, Szymon Sobczak, Michał Antoszczak, Miguel Prudêncio, Adam Huczyński|2024|Eur.J.Med.Chem.|263|115951|doi:10.1016/j.ejmech.2023.115951
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h0mpv
title: CCDC 2294517: Experimental Crystal Structure Determination

description: Related Article: Michał Sulik, Diana Fontinha, Dietmar Steverding, Szymon Sobczak, Michał Antoszczak, Miguel Prudêncio, Adam Huczyński|2024|Eur.J.Med.Chem.|263|115951|doi:10.1016/j.ejmech.2023.115951
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gt29p
title: CCDC 2288212: Experimental Crystal Structure Determination

description: Related Article: Inga-Alexandra Bischoff, Bernd Morgenstern, Michael Zimmer, Aylin Koldemir, Rainer Pöttgen, André Schäfer|2023|Dalton Trans.|52|17928|doi:10.1039/D3DT02664G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2gt2bq
title: CCDC 2288213: Experimental Crystal Structure Determination

description: Related Article: Inga-Alexandra Bischoff, Bernd Morgenstern, Michael Zimmer, Aylin Koldemir, Rainer Pöttgen, André Schäfer|2023|Dalton Trans.|52|17928|doi:10.1039/D3DT02664G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h1jnr
title: CCDC 2295384: Experimental Crystal Structure Determination

description: Related Article: Ruchun Yang, Yongge Xiong, Si Deng, Jiang Bai, Xian-Rong Song, Qiang Xiao|2023|RSC Advances|13|33495|doi:10.1039/D3RA06747E
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h1p8j
title: CCDC 2295527: Experimental Crystal Structure Determination

description: Related Article: Luisa Leinauer, Giorgio Parla, Julian Messelbeger, Alberto Herrera, Frank W. Heinemann, Jens Langer, Ilya Chuchelkin, Alexander Grasruck, Sibylle Frieß, Ahmed Chelouan, Konstantin Gavrilov, Romano Dorta|2023|Chem.Commun.|59|14451|doi:10.1039/D3CC04972H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2h1p9k
title: CCDC 2295528: Experimental Crystal Structure Determination

description: Related Article: Luisa Leinauer, Giorgio Parla, Julian Messelbeger, Alberto Herrera, Frank W. Heinemann, Jens Langer, Ilya Chuchelkin, Alexander Grasruck, Sibylle Frieß, Ahmed Chelouan, Konstantin Gavrilov, Romano Dorta|2023|Chem.Commun.|59|14451|doi:10.1039/D3CC04972H
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.24739581
title: CS Home Training data.xlsx

description: After baseline measurements in-lab, participants were sent home to train for several months (subacute (SA): 4.9±0.6 months [mean ± SD]; chronic (CH): 6.8±4.0 months). They used their personal computers with a chin/forehead-rest provided by the lab, which they were instructed to position 42cm away from their display during training. Participants performed 300 trials of their assigned training tasks (Static, Motion or Flicker) per location per day, at least five days per week, and they emailed their data log files back to the lab for analysis every week. During home training sessions, they were instructed to stay fixated on the fixation spot and warned that inadequate fixation accuracy could limit recovery.Session thresholds were calculated by fitting a Weibull function with a 72.5 percent correct performance threshold criterion. After participants’ thresholds improved consistently for at least 20 sessions, we moved their training stimulus 1˚ deeper into the blind field along the x-axis (Cartesian coordinate space). Because the diameter of the stimulus is 2.5 ˚, the new training location had ~80% overlap with the original training location.<i> </i>Once participants trained for about 4 months, with at least one improved location (defined as consistently good contrast thresholds at that location), they were brought back to the lab, and performance at all home-trained locations was verified with eye tracker-enforced fixation control. We aimed for a similar number of training sessions at the blind-field locations of interest before scheduling people to return for in-lab performance verification. However, the amount of time elapsed until the return visit did vary, as it was affected by the individual’s rate of improvement, their work/family schedules, and ability to travel to our single study site (participants originated from across the entire United States and Canada). All participants were best corrected using glasses or contact lenses during testing and training. The Research Subjects Review Board approved study procedures at the University of Rochester, which were conducted as per the Declaration of Helsinki, with written informed consent obtained from each participant, and participation was voluntary.<br>
DOI: 10.6084/m9.figshare.24739581.v1
title: CS Home Training data.xlsx

description: After baseline measurements in-lab, participants were sent home to train for several months (subacute (SA): 4.9±0.6 months [mean ± SD]; chronic (CH): 6.8±4.0 months). They used their personal computers with a chin/forehead-rest provided by the lab, which they were instructed to position 42cm away from their display during training. Participants performed 300 trials of their assigned training tasks (Static, Motion or Flicker) per location per day, at least five days per week, and they emailed their data log files back to the lab for analysis every week. During home training sessions, they were instructed to stay fixated on the fixation spot and warned that inadequate fixation accuracy could limit recovery.Session thresholds were calculated by fitting a Weibull function with a 72.5 percent correct performance threshold criterion. After participants’ thresholds improved consistently for at least 20 sessions, we moved their training stimulus 1˚ deeper into the blind field along the x-axis (Cartesian coordinate space). Because the diameter of the stimulus is 2.5 ˚, the new training location had ~80% overlap with the original training location.<i> </i>Once participants trained for about 4 months, with at least one improved location (defined as consistently good contrast thresholds at that location), they were brought back to the lab, and performance at all home-trained locations was verified with eye tracker-enforced fixation control. We aimed for a similar number of training sessions at the blind-field locations of interest before scheduling people to return for in-lab performance verification. However, the amount of time elapsed until the return visit did vary, as it was affected by the individual’s rate of improvement, their work/family schedules, and ability to travel to our single study site (participants originated from across the entire United States and Canada). All participants were best corrected using glasses or contact lenses during testing and training. The Research Subjects Review Board approved study procedures at the University of Rochester, which were conducted as per the Declaration of Helsinki, with written informed consent obtained from each participant, and participation was voluntary.<br>
DOI: 10.5281/zenodo.10305572
title: Colville River Delta Sea Ice Model and Output Data Files

description: In this study, we used a 1D Delft3D-FLOW model to simulate the temporal development of the Colville River Delta, AK during the most active Arctic seasons. Simulations focused on the deltaic clinoform (i.e., the cross-sectional view of a delta) and used a floating barge structure to mimic the effects of sea ice on surface waters. Delft3D simulations were coupled with modules written in MATLAB and outputs were process in MATLAB.
The dataset includes an example model run file (Delft3D-FLOW and MATLAB) and output of results from simulations used to assess Arctic delta development under sea ice.  
Files include:

Example Delft3D-FLOW model setup file, MATLAB run script, and ice files for a 1500-year simulation.
Processed MATLAB structures and metadata for model results

Long-term Delta Developmental Outputs (1500-year simulations)

Ice-free
Ice-affected
Ice-free with waves
Ice-affected with waves
Varying Sea Ice Characteristics Outputs (500-year simulations)

Ice matrix (six simulations)
Future Arctic Delta Scenarios Outputs (450-year simulations)  

Scenario A
Scenario B
DOI: 10.5281/zenodo.10305573
title: Colville River Delta Sea Ice Model and Output Data Files

description: In this study, we used a 1D Delft3D-FLOW model to simulate the temporal development of the Colville River Delta, AK during the most active Arctic seasons. Simulations focused on the deltaic clinoform (i.e., the cross-sectional view of a delta) and used a floating barge structure to mimic the effects of sea ice on surface waters. Delft3D simulations were coupled with modules written in MATLAB and outputs were process in MATLAB.
The dataset includes an example model run file (Delft3D-FLOW and MATLAB) and output of results from simulations used to assess Arctic delta development under sea ice.  
Files include:

Example Delft3D-FLOW model setup file, MATLAB run script, and ice files for a 1500-year simulation.
Processed MATLAB structures and metadata for model results

Long-term Delta Developmental Outputs (1500-year simulations)

Ice-free
Ice-affected
Ice-free with waves
Ice-affected with waves
Varying Sea Ice Characteristics Outputs (500-year simulations)

Ice matrix (six simulations)
Future Arctic Delta Scenarios Outputs (450-year simulations)  

Scenario A
Scenario B
DOI: 10.6084/m9.figshare.24777990.v1
title: spectrogram_Cz_all_subjects.zip

description: EEG recordings from 14 patients undergoing an infusion of the drug propofol. This dataset contains the computed spectrogram of each patient from the Cz recording electrode. Time is encoded relative to the moment of loss of consciousness, i.e. LOC occurs at 0 s.
DOI: 10.6084/m9.figshare.24201129.v3
title: How Does ChatGPT-3.5 Compare with Developers When Answering Questions and Revising Software?

description: This folder contains all the experiment results and programs for our research to investigate how ChatGPT3.5 performs compared to Developers when answering technical questions and revising software based on maintenance request.
DOI: 10.6084/m9.figshare.24201129.v4
title: How Does ChatGPT-3.5 Compare with Developers When Answering Questions and Revising Software?

description: This folder contains all the experiment results and programs for our research to investigate how ChatGPT3.5 performs compared to Developers when answering technical questions and revising software based on maintenance request.
DOI: 10.5281/zenodo.10310083
title: Table 1. DEGs TNF vs CTRL
DOI: 10.5281/zenodo.10310082
title: Table 1. DEGs TNF vs CTRL
DOI: 10.5063/f18g8j5n
title: TREAM: Time series of freshwater macroinvertebrate abundances and site characteristics of European streams and rivers

description: Freshwater macroinvertebrates are a diverse group that play many key ecological roles, including accelerating nutrient cycling, filtering water, controlling aquatic primary producers, and providing food for predators. Since they rapidly respond to environmental changes, macroinvertebrate community composition is a commonly used indicator of water quality. In Europe, efforts to improve water quality following environmental legislation, primarily starting in the 1980s, may have driven a recovery of macroinvertebrate communities. Towards understanding temporal changes of these organisms, we compiled the TREAM database (Time seRies of European freshwAter Macroinvertebrates). The TREAM database consists of whole macroinvertebrate community time series from 1,816 river and stream sites (mean length of 19.2 years with 14.9 sampling years) of 22 European countries sampled between 1968 and 2020. In total, the data include &gt;93 million sampled individuals of 2,648 taxa from 959 genera and 212 families. These data can be used to ask a wide range of questions from identifying drivers of the population dynamics of specific taxa to assessing the success of legislative and management restoration efforts.
DOI: 10.18112/openneuro.ds004654.v1.0.1
title: Rates of cerebral protein synthesis in subjects with fragile X syndrome
DOI: 10.18112/openneuro.ds004730.v1.0.0
title: Effects of propofol anesthesia on rates of cerebral protein synthesis
DOI: 10.18112/openneuro.ds004731.v1.0.0
title: Rates of cerebral protein synthesis and memory formation during sleep
DOI: 10.18112/openneuro.ds004733.v1.0.0
title: Rates of cerebral protein synthesis in stages of sleep
DOI: 10.5281/zenodo.10310178
title: Table S2: Gene set enrichment analysis and KEGG
DOI: 10.5281/zenodo.10310179
title: Table S2: Gene set enrichment analysis and KEGG
DOI: 10.6084/m9.figshare.22149266
title: Arkin & Márquez Repo

description: Repository for Arkin & Márquez, The effects of preformed vitamin A and provitamin A carotenoid supplementation on tadpoles of the poison frog Phyllobates vittatus. Three datasets are provided in tsv formal, as well as the code used to analyze and visualize them in R format.
DOI: 10.6084/m9.figshare.22149266.v1
title: Datasets

description: Data collected from tadpole measurements and monitoring.
DOI: 10.6084/m9.figshare.22149266.v2
title: Arkin & Márquez Repo

description: Repository for Arkin & Márquez, The effects of preformed vitamin A and provitamin A carotenoid supplementation on tadpoles of the poison frog Phyllobates vittatus. Three datasets are provided in tsv formal, as well as the code used to analyze and visualize them in R format.
DOI: 10.6084/m9.figshare.24129054
title: <b>Lessons from assembling UCEs: a comparison of common methods and the case of </b><b><i>Clavinomia </i></b><b>(Halictidae)</b>

description: This readme.txt file was generated on 2023-NOV-29 by Silas BossertThis repository contains supplementary files associated with the research article:Lessons from assembling UCEs: a comparison of common methods and the case of Clavinomia (Halictidae)by Silas Bossert, Alain Pauly, Bryan N. Danforth, Michael C. Orr, and Elizabeth A. MurrayFor questions and/or concerns please contact the lead author of the paper under silas.bossert [at] wsu.eduThis repository consists of 15 files.###1. 01_Supplemental_Information.pdf###This Pdf file contains supplementary information to the main article. The file is the same as the one provided on the website of the journal.###2. 02_Assembly_Comparisons.xlsx###This spreadsheet contains raw data on alignment and UCE statistics of the examined and compared UCE data sets.###3. 03_Distances_genetrees_speciestrees.R###This is an R script which was developed to efficiently compute phylogenetic distances between individual gene trees and a given refernce tree, even if the gene tree has incomplete taxon sampling. The R script is annoated; if questions arise, please contact the corresponding author.###4. 04_Beastfile_1.xml###The input file for the Beast analyses.###5. 05_Beast_chronogram.tre###The chronogram, which was estimated with Beast.###6. 06_Gene_trees.tar.gz###An archive which contains all individual gene trees estimated in the study.###7. 07_Species_trees.tar.gz###An archive which contains all species trees estimated in the present study, except for the Beast chronogram, which is provided as a separate file.###8. 08_Alignments_63_taxa.tar.gz###The alignments for the 63 taxon sets derived from assemblies of all five assemblers used in the present study (ABySS, HybPiper, SPAdes, Trinity, Velvet).###9. 09_Alignments_75_taxa.tar.gz###The alignments for the 75 taxon sets derived from assemblies of all five assemblers used in the present study (ABySS, HybPiper, SPAdes, Trinity, Velvet).###10. 10_Assemblies_Abyss.rar###The assembled, contiguous sequences which were generated with the ABySS assembly software.###1. 11_Assemblies_HybPiper.rar###The assembled, contiguous sequences which were generated with the HybPiper pipeline.###12. 12_Assemblies_SPAdes.rar###The assembled, contiguous sequences which were generated with the SPAdes assembly software.###13. 13_Assemblies_Trinity.rar###The assembled, contiguous sequences which were generated with the Trinity assembly software.###14. 14_Assemblies_Velvet.rar###The assembled, contiguous sequences which were generated with the Velvet assembly software.###15. 15_Other_Assemblies.rar###This archive contains 12 additional assembly files which were derived from other studies. See the Supplementary Information or the main article for details on the assemblies.
DOI: 10.6084/m9.figshare.24129054.v1
title: <b>Lessons from assembling UCEs: a comparison of common methods and the case of </b><b><i>Clavinomia </i></b><b>(Halictidae)</b>

description: This readme.txt file was generated on 2023-NOV-29 by Silas BossertThis repository contains supplementary files associated with the research article:Lessons from assembling UCEs: a comparison of common methods and the case of Clavinomia (Halictidae)by Silas Bossert, Alain Pauly, Bryan N. Danforth, Michael C. Orr, and Elizabeth A. MurrayFor questions and/or concerns please contact the lead author of the paper under silas.bossert [at] wsu.eduThis repository consists of 15 files.###1. 01_Supplemental_Information.pdf###This Pdf file contains supplementary information to the main article. The file is the same as the one provided on the website of the journal.###2. 02_Assembly_Comparisons.xlsx###This spreadsheet contains raw data on alignment and UCE statistics of the examined and compared UCE data sets.###3. 03_Distances_genetrees_speciestrees.R###This is an R script which was developed to efficiently compute phylogenetic distances between individual gene trees and a given refernce tree, even if the gene tree has incomplete taxon sampling. The R script is annoated; if questions arise, please contact the corresponding author.###4. 04_Beastfile_1.xml###The input file for the Beast analyses.###5. 05_Beast_chronogram.tre###The chronogram, which was estimated with Beast.###6. 06_Gene_trees.tar.gz###An archive which contains all individual gene trees estimated in the study.###7. 07_Species_trees.tar.gz###An archive which contains all species trees estimated in the present study, except for the Beast chronogram, which is provided as a separate file.###8. 08_Alignments_63_taxa.tar.gz###The alignments for the 63 taxon sets derived from assemblies of all five assemblers used in the present study (ABySS, HybPiper, SPAdes, Trinity, Velvet).###9. 09_Alignments_75_taxa.tar.gz###The alignments for the 75 taxon sets derived from assemblies of all five assemblers used in the present study (ABySS, HybPiper, SPAdes, Trinity, Velvet).###10. 10_Assemblies_Abyss.rar###The assembled, contiguous sequences which were generated with the ABySS assembly software.###1. 11_Assemblies_HybPiper.rar###The assembled, contiguous sequences which were generated with the HybPiper pipeline.###12. 12_Assemblies_SPAdes.rar###The assembled, contiguous sequences which were generated with the SPAdes assembly software.###13. 13_Assemblies_Trinity.rar###The assembled, contiguous sequences which were generated with the Trinity assembly software.###14. 14_Assemblies_Velvet.rar###The assembled, contiguous sequences which were generated with the Velvet assembly software.###15. 15_Other_Assemblies.rar###This archive contains 12 additional assembly files which were derived from other studies. See the Supplementary Information or the main article for details on the assemblies.
DOI: 10.34740/kaggle/dsv/7157588
title: Daily Public Opinion on Israel-Palestine War
DOI: 10.6084/m9.figshare.24778146
title: Ribeiro et al., 2023

description: Dataset
DOI: 10.25345/c5d795n33
title: MassIVE MSV000093613 - Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer
title: Contains files from manuscript titled 'Fast and Deep Phosphoproteome Analysis with the Orbitrap Astral Mass Spectrometer'. Includes mouse and human phosphoproteomics with Orbitrap Astral and mouse proteomics with Orbitrap Eclipse.