cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16988222
title: Experiment data from A chronology of subterranean clover burr detachment mechanics and implications for seed harvestability

description: Burr retention strength, peduncle strength and burr moisture content data collected in this study
DOI: 10.6084/m9.figshare.16988212
title: Supplementary Table 1_Sterken et al 2021.xlsx

description: RNA was isolated from three pools of BT-20 WT cells and three BT-20 <i>CEBPB</i>-ko clones, using the RNeasy Plus Mini Kit (QIAGEN). Quality and quantity of RNA was determined using Agilent’s Bioanalyzer 2100 in combination with the RNA 6000 nano chip (Agilent). Library preparation was done using Illumina’s TruSeq RNA v2 kit following the manufacturer’s description. The libraries were quality checked and quantified using Bioanalyzer 2100 in combination with the DNA 7500 kit (Agilent). Sequencing was done on a HiSeq2500 in 50 bp, single-end sequencing, high-output mode. Sequence information was extracted using bcl2fastq v1.8.3 (Illumina), Sequencing resulted in around 50 million reads per sample. Quality of the reads was checked using FastQC (v. 0.11) and filtering and trimming of low-quality reads was performed using Trimmomatic (v. 0.33). Trimmed reads were aligned to the GRCh38/mm10 genome (genome annotation from ensemble release 92) using STAR aligner v. 2.6.0b<sup>60</sup>. Identification of differentially expressed genes (DEGs) was done using the R package DESeq2 <sup>27</sup>. The resulting p-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate<sup>61</sup>. Genes were regarded as differentially expressed if adjusted p-values were CEBPB WT vs <i>CEBPB</i>-ko. The t-statistic mean of the genes was computed for each hallmark gene set using a permutation test with 1000 replications.
DOI: 10.6084/m9.figshare.16988212.v1
title: Supplementary Table 1_Sterken et al 2021.xlsx

description: RNA was isolated from three pools of BT-20 WT cells and three BT-20 <i>CEBPB</i>-ko clones, using the RNeasy Plus Mini Kit (QIAGEN). Quality and quantity of RNA was determined using Agilent’s Bioanalyzer 2100 in combination with the RNA 6000 nano chip (Agilent). Library preparation was done using Illumina’s TruSeq RNA v2 kit following the manufacturer’s description. The libraries were quality checked and quantified using Bioanalyzer 2100 in combination with the DNA 7500 kit (Agilent). Sequencing was done on a HiSeq2500 in 50 bp, single-end sequencing, high-output mode. Sequence information was extracted using bcl2fastq v1.8.3 (Illumina), Sequencing resulted in around 50 million reads per sample. Quality of the reads was checked using FastQC (v. 0.11) and filtering and trimming of low-quality reads was performed using Trimmomatic (v. 0.33). Trimmed reads were aligned to the GRCh38/mm10 genome (genome annotation from ensemble release 92) using STAR aligner v. 2.6.0b<sup>60</sup>. Identification of differentially expressed genes (DEGs) was done using the R package DESeq2 <sup>27</sup>. The resulting p-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate<sup>61</sup>. Genes were regarded as differentially expressed if adjusted p-values were CEBPB WT vs <i>CEBPB</i>-ko. The t-statistic mean of the genes was computed for each hallmark gene set using a permutation test with 1000 replications.
DOI: 10.5281/zenodo.5674900
title: Replication Package For Assessing the Effect of Programming Language and Task On Eye Movements

description: A replication package for Assessing the Effect of Programming Language and Task On Eye Movements containing the aggregated dataset, stimuli, and scripts to calculate the results presented in the paper.
DOI: 10.5281/zenodo.5674899
title: Replication Package For Assessing the Effect of Programming Language and Task On Eye Movements

description: A replication package for Assessing the Effect of Programming Language and Task On Eye Movements containing the aggregated dataset, stimuli, and scripts to calculate the results presented in the paper.
DOI: 10.18112/openneuro.ds003887.v1.0.0
title: Capacity for movement is a major organisational principle in object representations: EEG data from Experiment 3
DOI: 10.15161/oar.it/74240
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.18112/openneuro.ds003885.v1.0.0
title: Capacity for movement is a major organisational principle in object representations: EEG data from Experiment 2
DOI: 10.5281/zenodo.5674587
title: Bridgmanite is nearly dry at the top of the lower mantle

description: Bridgmanite is nearly dry at the top of the lower mantle
DOI: 10.5281/zenodo.5674586
title: Bridgmanite is nearly dry at the top of the lower mantle

description: Bridgmanite is nearly dry at the top of the lower mantle
DOI: 10.18112/openneuro.ds003885.v1.0.1
title: Capacity for movement is a major organisational principle in object representations: EEG data from Experiment 2
DOI: 10.25345/c5wc58
title: MassIVE MSV000088347 - pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation
title: Interpreting large-scale glycoproteomic data for intact glycopeptide identification has been tremendously advanced by software tools. However, software tools for quantitative analysis of intact glycopeptides remain lagging behind, which greatly hinders exploring the differential expression and functions of site-specific glycosylation in organisms. Here, we report pGlycoQuant, a generic software tool for accurate and convenient quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant enables intact glycopeptide quantitation with very low missing values via a deep residual network, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco3, Byonic and MSFragger-Glyco. The pGlycoQuant-based site-specific N-glycoproteomic study conducted here quantifies 6435 intact N-glycopeptides in three hepatocellular carcinoma cell lines with different metastatic potentials and, together with in vitro molecular biology experiments, illustrates core fucosylation at site 979 of the L1 cell adhesion molecule (L1CAM) as a potential regulator of HCC metastasis. pGlycoQuant is freely available at https://github.com/expellir-arma/pGlycoQuant_V1.1_released/archive/refs/tags/pGlycoQuant_V1.1_released.zip. We have demonstrated pGlycoQuant to be a powerful tool for the quantitative analysis of site-specific glycosylation and the exploration of potential glycosylation-related biomarker candidates, and we expect further applications in glycoproteomic studies.
DOI: 10.6084/m9.figshare.14637804
title: Metadata_CLBM_elemental_isotope_Lienart_et_al_2021_Biogeochemistry.csv

description: This dataset present elemental Carbon, Nitrogen, Phosphorus) and carbon and nitrogen isotope (delta-13C, delta-15N) composition of the filamentous green algae from the genus Cladophora spp. and the blue mussel Mytilus sp. from three contrasted regions (and various stations) of the Baltic Sea. The time series are spaning 8 to 24 years with one value per year and region/station. <br>Table 1 : Cladophora C, N and P contents and delta-13C, delta-15N ratios. <br>Table 2: Mytilus C and N contents and delta-13C, delta-15N ratios. <br>Table 3: Mytilus P content (measured on different individuals)<br>
DOI: 10.17037/data.00002623
title: Diagnosis/symptom codelist - fatigue codes

description: Read codes for fatigue (including symptoms of fatigue and diagnoses of post-viral fatigue and ME/CFS). These are made available to support the paper, "Incidence of Lyme disease in the United Kingdom and association with fatigue: a population-based, historical cohort study".
DOI: 10.5281/zenodo.5674685
title: Isoprene mixing ratio in ambient air across the Southern Ocean in the austral summer of 2016/2017, during the Antarctic Circumnavigation Expedition (ACE).

description: <strong>Dataset abstract</strong> This dataset contains the mixing ratios of isoprene (C5H8) in ambient air measured during the Antarctic Circumnavigation Expedition around the Southern Ocean in the austral summer of 2016/2017 using the iDirac, an autonomous gas chromatograph (Bolas et al., 2020). Samples were collected at a temporal resolution of approximately 10 minutes, with sizeable gaps in the dataset during Legs 1 and 3 due to instrument malfunction. Isoprene represents one of the largest biogenic emissions on the planet. While the magnitude and mechanism of its emissions on land are well established, there is still large uncertainty on the drivers of marine isoprene emissions. This dataset, consisting of continuous measurements at a relatively high temporal resolution, represents a unique opportunity to better understand marine isoprene emissions in the Southern Ocean. <strong>Dataset contents</strong> ace_isoprene_mixing_ratio_ambient_air_v1.1.csv, data file, comma-separated values data_file_header.txt, metadata, text README.txt, metadata, text change_log.txt, metadata, text <strong>Change log</strong> v1.1 - data files updated more accurate isoprene quantification from improved chromatogram baseline removal v1.0 - initial release of dataset
description: The Antarctic Circumnavigation Expedition was made possible by funding from the Swiss Polar Institute and Ferring Pharmaceuticals.
description: {"references": ["David W H Walton, & Jenny Thomas. (2018, November 22). Cruise Report - Antarctic Circumnavigation Expedition (ACE) 20th December 2016 - 19th March 2017 (Version 1.0). Zenodo. http://doi.org/10.5281/zenodo.1443511", "Bolas, C. G., Ferracci, V., Robinson, A. D., Mead, M. I., Nadzir, M. S. M., Pyle, J. A., Jones, R. L., and Harris, N. R. P.: iDirac: a field-portable instrument for long-term autonomous measurements of isoprene and selected VOCs, Atmos. Meas. Tech., 13, 821\u2013838, https://doi.org/10.5194/amt-13-821-2020, 2020."]}
DOI: 10.5281/zenodo.3993390
title: Isoprene mixing ratio in ambient air across the Southern Ocean in the austral summer of 2016/2017, during the Antarctic Circumnavigation Expedition (ACE).

description: <strong>Dataset abstract</strong> This dataset contains the mixing ratios of isoprene (C5H8) in ambient air measured during the Antarctic Circumnavigation Expedition around the Southern Ocean in the austral summer of 2016/2017 using the iDirac, an autonomous gas chromatograph (Bolas et al., 2020). Samples were collected at a temporal resolution of approximately 10 minutes, with sizeable gaps in the dataset during Legs 1 and 3 due to instrument malfunction. Isoprene represents one of the largest biogenic emissions on the planet. While the magnitude and mechanism of its emissions on land are well established, there is still large uncertainty on the drivers of marine isoprene emissions. This dataset, consisting of continuous measurements at a relatively high temporal resolution, represents a unique opportunity to better understand marine isoprene emissions in the Southern Ocean. <strong>Dataset contents</strong> ace_isoprene_mixing_ratio_ambient_air_v1.1.csv, data file, comma-separated values data_file_header.txt, metadata, text README.txt, metadata, text change_log.txt, metadata, text <strong>Change log</strong> v1.1 - data files updated more accurate isoprene quantification from improved chromatogram baseline removal v1.0 - initial release of dataset
description: The Antarctic Circumnavigation Expedition was made possible by funding from the Swiss Polar Institute and Ferring Pharmaceuticals.
description: {"references": ["David W H Walton, & Jenny Thomas. (2018, November 22). Cruise Report - Antarctic Circumnavigation Expedition (ACE) 20th December 2016 - 19th March 2017 (Version 1.0). Zenodo. http://doi.org/10.5281/zenodo.1443511", "Bolas, C. G., Ferracci, V., Robinson, A. D., Mead, M. I., Nadzir, M. S. M., Pyle, J. A., Jones, R. L., and Harris, N. R. P.: iDirac: a field-portable instrument for long-term autonomous measurements of isoprene and selected VOCs, Atmos. Meas. Tech., 13, 821\u2013838, https://doi.org/10.5194/amt-13-821-2020, 2020."]}
DOI: 10.17037/data.00002625
title: Code lists for: "Incidence of Lyme disease in the United Kingdom and association with fatigue: a population-based, historical cohort study"
DOI: 10.17037/data.00002624
title: Diagnosis codelist - Lyme disease codes

description: Read codes for Lyme disease. These support a publication titled "Incidence of Lyme disease in the United Kingdom and association with fatigue: a population-based, historical cohort study".
DOI: 10.7479/7vak-qz53
title: Geschäftsbericht 2020

description: Der Geschäftsbericht des Museums für Naturkunde Berlin erscheint in deutscher Sprache und beinhaltet neben Gecshäftszahlen auch Highlights in Text und Bild.
DOI: 10.6084/m9.figshare.16552707.v1
title: Supplemental Table 4: β-blocker and α-blocker drug log2-surviving fraction included in the compound library screens.

description: log2-surviving fraction (s.f) is shown following treatment of OVCAR4, Ov4Cis and Ov4Carbo with the indicated drugs. Library = s.f. in wells treated with compound library drug compared to vehicle treatment. Library + adenovirus = s.f. in wells treated with compound library drug + adenovirus compared to adenovirus alone. For the purposes of this study, a compound was considered as a hit if s.f. &lt; -2 only for library + adenovirus treatments.
DOI: 10.6084/m9.figshare.16552671
title: Supplementary Table 1: Log2-surviving fraction of the drug screen in cisplatin-resistant HGSC

description: <b>Supplementary Table 1: Log2-surviving fraction of the drug screen in cisplatin-resistant HGSC</b>Complete list of log2-surviving fraction for each well of the compound library screen in OVCAR4 and Ov4Cis cells. Results for all experimental conditions are shown including control-treated wells. log2-surviving fraction (s.f) is shown following treatment of OVCAR4 and Ov4Cis with the indicated drugs. Library = s.f. in wells treated with compound library drug compared to vehicle treatment. Library + adenovirus = s.f. in wells treated with compound library drug + adenovirus compared to adenovirus alone.<br>
DOI: 10.6084/m9.figshare.16552683.v1
title: Supplementary Table 2: Log2-surviving fraction of the drug screen in carboplatin-resistant HGSC

description: Complete list of log2-surviving fraction for each well of the compound library screen in OVCAR4 and Ov4Carbo cells. Results for all experimental conditions are shown including control-treated wells. log2-surviving fraction (s.f) is shown following treatment of OVCAR4 and Ov4Cis with the indicated drugs. Library = s.f. in wells treated with compound library drug compared to vehicle treatment. Library + adenovirus = s.f. in wells treated with compound library drug + adenovirus compared to adenovirus alone.
DOI: 10.6084/m9.figshare.16552695
title: Supplementary Table 3: Hit drugs identified in the both compound library screens comparing OVCAR4 to Ov4Cis and also OVCAR4 to Ov4Carbo

description: Log2-surviving fraction (s.f) is shown following treatment with the indicated drugs. Library = surviving fraction (s.f.) in wells treated with compound library drug compared to vehicle treatment. Library + dl922-947 = s.f. in wells treated with compound library drug + dl922-947 compared to dl922-947 alone.
DOI: 10.6084/m9.figshare.16552695.v1
title: Supplementary Table 3: Hit drugs identified in the both compound library screens comparing OVCAR4 to Ov4Cis and also OVCAR4 to Ov4Carbo

description: Log2-surviving fraction (s.f) is shown following treatment with the indicated drugs. Library = surviving fraction (s.f.) in wells treated with compound library drug compared to vehicle treatment. Library + dl922-947 = s.f. in wells treated with compound library drug + dl922-947 compared to dl922-947 alone.
DOI: 10.6084/m9.figshare.16552707
title: Supplemental Table 4: β-blocker and α-blocker drug log2-surviving fraction included in the compound library screens.

description: log2-surviving fraction (s.f) is shown following treatment of OVCAR4, Ov4Cis and Ov4Carbo with the indicated drugs. Library = s.f. in wells treated with compound library drug compared to vehicle treatment. Library + adenovirus = s.f. in wells treated with compound library drug + adenovirus compared to adenovirus alone. For the purposes of this study, a compound was considered as a hit if s.f. &lt; -2 only for library + adenovirus treatments.
DOI: 10.6084/m9.figshare.16552671.v1
title: Supplementary Table 1: Log2-surviving fraction of the drug screen in cisplatin-resistant HGSC

description: <b>Supplementary Table 1: Log2-surviving fraction of the drug screen in cisplatin-resistant HGSC</b>Complete list of log2-surviving fraction for each well of the compound library screen in OVCAR4 and Ov4Cis cells. Results for all experimental conditions are shown including control-treated wells. log2-surviving fraction (s.f) is shown following treatment of OVCAR4 and Ov4Cis with the indicated drugs. Library = s.f. in wells treated with compound library drug compared to vehicle treatment. Library + adenovirus = s.f. in wells treated with compound library drug + adenovirus compared to adenovirus alone.<br>
DOI: 10.6084/m9.figshare.16552683
title: Supplementary Table 2: Log2-surviving fraction of the drug screen in carboplatin-resistant HGSC

description: Complete list of log2-surviving fraction for each well of the compound library screen in OVCAR4 and Ov4Carbo cells. Results for all experimental conditions are shown including control-treated wells. log2-surviving fraction (s.f) is shown following treatment of OVCAR4 and Ov4Cis with the indicated drugs. Library = s.f. in wells treated with compound library drug compared to vehicle treatment. Library + adenovirus = s.f. in wells treated with compound library drug + adenovirus compared to adenovirus alone.
DOI: 10.23728/b2share.a7ddd84a3db146d3a5632408d4410c58
title: Participant dataset submitted by Ensembl_Compara

description: Participant dataset submitted by participant Ensembl_Compara for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.b8ce06ab6c994ce7a002373fe690960b
title: Participant dataset submitted by RSD

description: Participant dataset submitted by participant RSD for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.945ffadaae3545ffaabaf761366a5f2d
title: Participant dataset submitted by BBH

description: Participant dataset submitted by participant BBH for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.49ea3c4298624330a5866e8a7e364238
title: Participant dataset submitted by Sonicparanoid-sens

description: Participant dataset submitted by participant Sonicparanoid-sens for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.ffa92e38a43f47b78960629ffe5e3ebf
title: Participant dataset submitted by Sonicparanoid-mostsens

description: Participant dataset submitted by participant Sonicparanoid-mostsens for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.43d516593e434b2a927badcde4128850
title: Participant dataset submitted by Sonicparanoid-fast

description: Participant dataset submitted by participant Sonicparanoid-fast for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.1db874b7854f4d29a4e17dadceb7526b
title: Participant dataset submitted by Sonicparanoid

description: Participant dataset submitted by participant Sonicparanoid for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.12cdd91bd5c54c73a694e95046fc98ad
title: Participant dataset submitted by PANTHER__16__LDO__only

description: Participant dataset submitted by participant PANTHER__16__LDO__only for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.ce36272dd3c843ba99f12d9cd9568e3b
title: Participant dataset submitted by PANTHER_16_all

description: Participant dataset submitted by participant PANTHER_16_all for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.b281e1797c4a409abca1791e09902c59
title: Participant dataset submitted by OrthoMCL

description: Participant dataset submitted by participant OrthoMCL for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.5281/zenodo.5667551
title: Survey on the Future of the Barcamp Open Science (Dataset)

description: In September 2021, the Leibniz Research Alliance Open Science and Wikimedia Germany, as the organizer of Barcamp Open Science (www.barcamp-open-science.eu), conducted a survey on the future direction of this event. The resulting survey data is located in this dataset: The questionnaire as PDF A summary of the results as XLS / ODS All answers as CSV (personal "referrer URL" have been replaced by an empty string) A report on how the results are taken up can be found here: www.leibniz-openscience.de/future-of-the-barcamp-open-science-a-survey-and-what-we-take-from-it Lambert Heller had the lead in creating and evaluating the questionnaire.
DOI: 10.23728/b2share.ae81c6f90454449db862565d64715f82
title: Participant dataset submitted by OrthoInspector 3

description: Participant dataset submitted by participant OrthoInspector for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.5281/zenodo.5667550
title: Survey on the Future of the Barcamp Open Science (Dataset)

description: In September 2021, the Leibniz Research Alliance Open Science and Wikimedia Germany, as the organizer of Barcamp Open Science (www.barcamp-open-science.eu), conducted a survey on the future direction of this event. The resulting survey data is located in this dataset: The questionnaire as PDF A summary of the results as XLS / ODS All answers as CSV (personal "referrer URL" have been replaced by an empty string) A report on how the results are taken up can be found here: www.leibniz-openscience.de/future-of-the-barcamp-open-science-a-survey-and-what-we-take-from-it Lambert Heller had the lead in creating and evaluating the questionnaire.
DOI: 10.23728/b2share.efbc0b3079d2483fa29a5609bc1c485e
title: Participant dataset submitted by OrthoFinder_MSA_v2.5.2

description: Participant dataset submitted by participant OrthoFinder_MSA_v2.5.2 for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.2d78bb74cada4f30afd5329b6373891f
title: Participant dataset submitted by OMA_Pairs

description: Participant dataset submitted by participant OMA_Pairs for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.502431215a46442cb7bb72742d80dad3
title: Participant dataset submitted by OMA_Groups

description: Participant dataset submitted by participant OMA_Groups for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.b25b150487d34e788cb8975d892bf351
title: Participant dataset submitted by OMA_GETHOGs

description: Participant dataset submitted by participant OMA_GETHOGs for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.
DOI: 10.23728/b2share.f7e328acc2c742d189acb3b09f130205
title: Participant dataset submitted by InParanoid_Xenfix

description: Participant dataset submitted by participant InParanoid_Xenfix for 'Quest for Orthologs - 2020 Reference Proteomes' benchmarking event.