cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7684348
title: The glacier loss day as indicator for extreme glacier melt in 2022

description: Data and scripts to reproduce the plots in Voordendag, A., Prinz, R., Schuster, L., and Kaser, G.: Brief communication: The glacier loss day as indicator for extreme glacier melt in 2022, The Cryosphere Discuss. [preprint], in review, 2023 When using this dataset, please refer to the original publication in addition to this Zenodo repository.
DOI: 10.5281/zenodo.7685589
title: The glacier loss day as indicator for extreme glacier melt in 2022

description: Data and scripts to reproduce the plots in Voordendag, A., Prinz, R., Schuster, L., and Kaser, G.: Brief communication: The glacier loss day as indicator for extreme glacier melt in 2022, The Cryosphere Discuss. [preprint], in review, 2023 When using this dataset, please refer to the original publication in addition to this Zenodo repository.
DOI: 10.5281/zenodo.8252313
title: The glacier loss day as indicator for extreme glacier melt in 2022

description: Data and scripts to reproduce the plots in Voordendag, A., Prinz, R., Schuster, L., and Kaser, G.: Brief communication: Brief communication: The Glacier Loss Day as indicator for a record negative glacier mass balance in 2022, The Cryosphere, 2023 When using this dataset, please refer to the original publication in addition to this Zenodo repository.
DOI: 10.26106/908a-c237
title: The gut archeobiome - FASTQ files

description: archeobiome sequencing data of children with Crohn's disease - FASTQ files
DOI: 10.26106/s9pq-3a43
title: The gut mycobiome - FASTQ files

description: Data includes FASTQ files from the gut mycobiome in children in relation to the clinical activity of Crohn's disease
DOI: 10.26106/93z7-4545
title: Proteomic profiling of exosomes derived from pancreatic beta-cells cultured under hyperglycemia

description: The raw MS data files were processed using Max Quant software (version 1.6.7.0). Peak lists were searched against the forward and reverse Swissprot database (Homo sapiens, 20 394 sequences downloaded on February 8, 2021) using the integrated Andromeda search engine . The false discovery rate (FDR) for the peptide and protein identification was set to 1%. All proteins that cannot be distinguished based on the identified peptides were merged into one protein group. Relative quantification and normalization were performed with the MaxLFQ label-free algorithm. The MaxQuant output table was further processed with the use of the Perseus platform (version 1.6.15.0). The proteins identified in the decoy database, contaminants, and proteins only identified by site were filtered out. All bioinformatic analyses were executed on LFQ intensities transformed to a logarithmic scale with base two. The Student’s t-test with the permutation-based FDR set to 5% was used to reveal changes in protein abundances under NG and HG conditions. The statistical analysis was performed for the proteins with a minimum of 3 valid LFQ intensity values in both groups. Proteins were considered as a differential when they were identified based on at least 2 peptides and their fold change was of at least 1.5.
DOI: 10.26106/zpt7-xf45
title: Data from Miniatura 5 fellowship

description: Dane surowe oraz przeanalizowane, uzyskane w trakcie stażu naukowego Miniatura 5 "Metody inżynierii genetycznej jako narzędzie w badaniach nad molekularnym mechanizmem wpływu pęcherzyków zewnątrzkomórkowych z komórek iPS na komórki krwiotwórcze krwi pępowinowej"
DOI: 10.26106/vxzq-rb05
title: Dataset for the study : "Sertraline does not affect veracity judgment but increases behavioral engagement with true and fake news"

description: Dataset for the study "Sertraline does not affect veracity judgment but increases behavioral engagement with true and fake news". Funding: The research leading to these results has received funding from the EEA Financial Mechanism 2014-2021. Project registration number: 2019/35/J/HS6/03498.
DOI: 10.26106/hexd-nt30
title: Raw data for the paper : "Carbon footprint of the analytical laboratory and the three-dimensional approach to its reduction"

description: Surowe dane badawcze i metadane w pliku Excel na podstawie których powstał artykuł naukowy o numerze DOI: https://doi.org/10.1016/j.greeac.2023.100051
DOI: 10.26106/fbxw-rs73
title: Mit polityczny w kinie Korei Północnej 1948-2011: lista filmów Korei Północnej wraz z miejscem dostępu

description: Lista filmów Korei Północnej uporządkowana według dat. Zawiera tytuł, tytuł oryginalny, tytuł w romanizacji, reżysera, miejsce dostępu i oraz komentarz.
DOI: 10.26106/1s6v-t189
title: Protein disulfide isomerase A1 regulates fenestration dynamics in primary mouse liver sinusoidal endothelial cells (LSECs), proteomic dataset

description: Dataset for proteomic analysis of liver sinusoidal endothelial cells.
DOI: 10.5255/ukda-sn-856632
title: Climate Change Survey of Academic Researchers at UK Universities, 2022

description: Interest in the relationship between the activities of universities and action on climate change is growing, but until recently there has been little focus on the role of researchers, particularly with regards to how research practices and culture can enable or inhibit change. This study addresses this gap, exploring researchers’ perceptions of universities’ measures to tackle their own emissions, their own engagement on issues surrounding the climate crisis, and challenges and opportunities for researchers to contribute to them. We present findings from a large, mixed methods survey of 1,853 researchers from 127 UK universities across disciplines and career stages, including comparing responses across these professional differences, and analysis based on over 5,000 open text responses provided by the survey participants. The results show that while most have some knowledge of the actions being taken and feel that climate emergency declarations are making a (small) difference, many think not enough is being done. They feel that responsibility for university climate action sits across government, universities and research councils, but almost all researchers are also personally worried about climate change and want to do more themselves to address it. For the most part, they also strongly support climate advocacy by those engaged in research. Yet high workload, uncertainty about what actions to take, perceived lack of agency or power, inflexible university processes and pressure to travel are just some of the many barriers researchers face in taking action. The study highlights how these barriers can be overcome, and the steps universities and researchers can take to better incorporate climate action into their research culture and practices.
DOI: 10.21227/0v4q-nn37
title: Treatment Effect Estimation Benchmarks

description: This bundle contains 4 well known and established causal inference benchmark datasets in order to evaluate the performance of causal/treatment effect estimation methods. These datasets are: IHDP, Jobs, Twins and News. All datasets are already publicly available. This bundle merely collects them in a single location for ease of replication.IHDP is based on Infant Health Development Program (IHDP) clinical trial. Goal: predict the effect of receiving specialised childcare on cognitive test score of the infants. Introduced by [1].Jobs combines data from the National Supported Work Program and the Panel Study of Income Dynamics. Goal: predict the effect of job training on employement status. Introduced by [4].Twins consists of twin births in the US between 1989-1991. Goal: predict the effect of higher body mass on mortality. This specifically pre-processed data come from [3].News is a collection of news articles represented as bags of words. Goal: predict the effect of device type used to read the article on the user experience. Introduced by [2]. See respective references for more details about the datasets. References[1] J. L. Hill, ‘Bayesian Nonparametric Modeling for Causal Inference’, Journal of Computational and Graphical Statistics, vol. 20, no. 1, pp. 217–240, Jan. 2011, doi: 10.1198/jcgs.2010.08162.[2] F. D. Johansson, U. Shalit, and D. Sontag, ‘Learning representations for counterfactual inference’, in Proceedings of the 33rd International Conference on International Conference on Machine Learning - Volume 48, in ICML’16. New York, NY, USA: JMLR.org, Jun. 2016, pp. 3020–3029.[3] C. Louizos, U. Shalit, J. M. Mooij, D. Sontag, R. Zemel, and M. Welling, ‘Causal Effect Inference with Deep Latent-Variable Models’, Advances in Neural Information Processing Systems, vol. 30, 2017, Accessed: May 25, 2021. [Online]. Available: https://proceedings.neurips.cc/paper/2017/hash/94b5bde6de888ddf9cde6748ad2523d1-Abstract.html[4] J. A. Smith and P. E. Todd, ‘Does matching overcome LaLonde’s critique of nonexperimental estimators?’, Journal of Econometrics, vol. 125, no. 1–2, pp. 305–353, 2005.
DOI: 10.5281/zenodo.8252368
title: Example of Leica .lif dataset containing FLIM and TileScan data

description: This dataset contains two files, Intro.lif and Intro.lifext, that contain multiple acquisition datasets from a Leica microscope. Some of the datasets contain metadata about FLIM experiments. Bio-Formats currently reads these datasets incorrectly, it appears as if the offset for the actual pixel data is computed inaccurately, possibly due to the extra metadata present in some series.
DOI: 10.5281/zenodo.8252367
title: Example of Leica .lif dataset containing FLIM and TileScan data

description: This dataset contains two files, Intro.lif and Intro.lifext, that contain multiple acquisition datasets from a Leica microscope. Some of the datasets contain metadata about FLIM experiments. Bio-Formats currently reads these datasets incorrectly, it appears as if the offset for the actual pixel data is computed inaccurately, possibly due to the extra metadata present in some series.
DOI: 10.6084/m9.figshare.23968002
title: UAV Images

description: RGB and TIR images of the Meruelo landfill photogrammetric flight.
DOI: 10.5281/zenodo.8252388
title: Processed INSDC dataset for MOV analysis

description: A processed version of a mutation-annotated tree from open SARS-CoV-2 genomic data, originally compiled by UCSC researchers at https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/. This is used as input to an open-data version of the analysis in <em>A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes</em>.
DOI: 10.5281/zenodo.8252387
title: Processed INSDC dataset for MOV analysis

description: A processed version of a mutation-annotated tree from open SARS-CoV-2 genomic data, originally compiled by UCSC researchers at https://hgwdev.gi.ucsc.edu/~angie/UShER_SARS-CoV-2/. This is used as input to an open-data version of the analysis in <em>A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes</em>.
DOI: 10.5281/zenodo.4755973
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Faerthen Felix, https://orcid.org/0000-0002-2922-8637. Claims were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5281/zenodo.4768687
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Faerthen Felix, https://orcid.org/0000-0002-2922-8637. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.34740/kaggle/dsv/6312781
title: 2021 World Population (updated daily)
DOI: 10.17028/rd.lboro.23968005
title: Supplementary information for Effect of replacing television viewing with different intensities of physical activity on COVID-19 mortality risk: Short communication from UK Biobank

description: Supplementary files for article Effect of replacing television viewing with different intensities of physical activity on COVID-19 mortality risk: Short communication from UK BiobankAims: This study aimed to examine the theoretical effects of replacing television (TV) viewing with different intensities of physical activity on COVID-19 mortality risk using isotemporal substitution models. Methods: The analytical sample was composed of 359,756 UK Biobank participants. TV viewing and physical activity were assessed by self-report. Logistic regressions adjusted for covariates were used to model the effects of substituting an hour a day of TV viewing with an hour of walking, moderate-intensity physical activity (MPA) or vigorous-intensity physical activity (VPA) on COVID-19 mortality risk. Results: From 16 March 2020 to 12 November 2021, there were 879 COVID-19 deaths in the analytical sample. Substituting an hour a day of TV viewing with an hour of walking was associated with a 17% lower risk of COVID-19 mortality (odds ratio (OR)=0.83, 95% confidence interval (CI) 0.74–0.92). In sex-stratified analyses, the same substitution was associated with a lower risk in both men (OR=0.85, 95% CI 0.74–0.96) and women (OR=0.78, 95% CI 0.65–0.95). However, replacing an hour a day of TV viewing with an hour of MPA was only associated with a lower risk in women (OR=0.80, 95% CI 0.65–0.98). <b>Conclusions: Replacing TV viewing with walking was associated with a significant reduction in COVID-19 mortality risk. Public health authorities should consider promoting the replacement of TV viewing with walking as a protective strategy against COVID-19 mortality.</b>
DOI: 10.17028/rd.lboro.23968005.v1
title: Supplementary information for Effect of replacing television viewing with different intensities of physical activity on COVID-19 mortality risk: Short communication from UK Biobank

description: Supplementary files for article Effect of replacing television viewing with different intensities of physical activity on COVID-19 mortality risk: Short communication from UK BiobankAims: This study aimed to examine the theoretical effects of replacing television (TV) viewing with different intensities of physical activity on COVID-19 mortality risk using isotemporal substitution models. Methods: The analytical sample was composed of 359,756 UK Biobank participants. TV viewing and physical activity were assessed by self-report. Logistic regressions adjusted for covariates were used to model the effects of substituting an hour a day of TV viewing with an hour of walking, moderate-intensity physical activity (MPA) or vigorous-intensity physical activity (VPA) on COVID-19 mortality risk. Results: From 16 March 2020 to 12 November 2021, there were 879 COVID-19 deaths in the analytical sample. Substituting an hour a day of TV viewing with an hour of walking was associated with a 17% lower risk of COVID-19 mortality (odds ratio (OR)=0.83, 95% confidence interval (CI) 0.74–0.92). In sex-stratified analyses, the same substitution was associated with a lower risk in both men (OR=0.85, 95% CI 0.74–0.96) and women (OR=0.78, 95% CI 0.65–0.95). However, replacing an hour a day of TV viewing with an hour of MPA was only associated with a lower risk in women (OR=0.80, 95% CI 0.65–0.98). <b>Conclusions: Replacing TV viewing with walking was associated with a significant reduction in COVID-19 mortality risk. Public health authorities should consider promoting the replacement of TV viewing with walking as a protective strategy against COVID-19 mortality.</b>
DOI: 10.34740/kaggle/dsv/6312785
title: YouTube Trending Video Dataset (updated daily)
DOI: 10.6084/m9.figshare.23967999
title: Metagenomes Assembles Genomes from cultivated freshwater bacterial communities

description: This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL) were inoculated with lake bacteria.The DNA from each microcosm was collected from 100 mL, exracted with DNeasy PowerBiofilm Kit (Qiagen) and shotgun sequenced on Illumina Hiseq platform (paired end 150bp, 5GB per microcosms).Raw paired-end Illumina shotgun reads were pre-processed to remove low-quality bases and reads. Briefly, Trimmomatic v.0.36 was used to interleave paired-end reads, perform quality trimming (Phred score = 33) and to remove sequencing adaptors. Additional checks (<i>i.e</i>. <i>de novo</i> adapter identification with “bbmerge.sh” (“BBMap v.37.02) were performed in order to ensure that the datasets met the quality threshold necessary for assembly. The pre-processed reads were assembled with “metaSPAdes” v3.11.1 using the k-mer sizes 21, 33, 55, 77, 99, 127. Curated metagenomic datasets were mapped using “bbwrap.sh” (BBMap v. 37.02) (parameters: kfilter=31, subfilter=15, maxindel=80) against the assembled contigs (longer than 2.5 Kb) in a sample-dependent fashion. The resulting BAM files were used to generate contig abundance profiles with “jgi_summarize_bam_contig_depths” from “MetaBAT2” v2.12.1 (parameter percentIdentity = 97). The contigs and their abundance files were used for binning with “MetaBAT2” (default settings). Bin completeness, contamination and strain heterogeneity were estimated using “CheckM” v1.0.3 (using the “lineage_wf” workflow). Bins with estimated completeness above 40% and contamination below 5% were denominated as metagenome assembled genomes (MAGs, n = 122).
DOI: 10.6084/m9.figshare.23967999.v1
title: Metagenomes Assembles Genomes from cultivated freshwater bacterial communities

description: This dataset represents 122 Metagenomes-Assembled Genomes (MAGs) that were reconstructed from 20 individual microcosms in the context of understanding microbial community assembly processes. The cultivation media consisted in Artificial Lake Water (ALW) enriched with glucose and cellobiose (See details in Le Moigne et al., 2023, Ecology). The microcosms (200 mL) were inoculated with lake bacteria.The DNA from each microcosm was collected from 100 mL, exracted with DNeasy PowerBiofilm Kit (Qiagen) and shotgun sequenced on Illumina Hiseq platform (paired end 150bp, 5GB per microcosms).Raw paired-end Illumina shotgun reads were pre-processed to remove low-quality bases and reads. Briefly, Trimmomatic v.0.36 was used to interleave paired-end reads, perform quality trimming (Phred score = 33) and to remove sequencing adaptors. Additional checks (<i>i.e</i>. <i>de novo</i> adapter identification with “bbmerge.sh” (“BBMap v.37.02) were performed in order to ensure that the datasets met the quality threshold necessary for assembly. The pre-processed reads were assembled with “metaSPAdes” v3.11.1 using the k-mer sizes 21, 33, 55, 77, 99, 127. Curated metagenomic datasets were mapped using “bbwrap.sh” (BBMap v. 37.02) (parameters: kfilter=31, subfilter=15, maxindel=80) against the assembled contigs (longer than 2.5 Kb) in a sample-dependent fashion. The resulting BAM files were used to generate contig abundance profiles with “jgi_summarize_bam_contig_depths” from “MetaBAT2” v2.12.1 (parameter percentIdentity = 97). The contigs and their abundance files were used for binning with “MetaBAT2” (default settings). Bin completeness, contamination and strain heterogeneity were estimated using “CheckM” v1.0.3 (using the “lineage_wf” workflow). Bins with estimated completeness above 40% and contamination below 5% were denominated as metagenome assembled genomes (MAGs, n = 122).
DOI: 10.6084/m9.figshare.23968008
title: Meruelo UAV

description: RGB and TIR images of the Meruelo landfill photogrammetric flight.
DOI: 10.26106/1s2a-kz08
title: Data to figures and tables

description: The file contains research data for figures 1 and 2 in the article: Gawedzka A, Grandys M, Duda K, Zapart-Bukowska J, Zoladz J.A, Majerczak J. "Plasma BCAA concentrations during exercise of varied intensities in young healthy men - the impact of endurance training", article is under review
DOI: 10.5281/zenodo.8252415
title: A biorefinery model for the production of oil and biomethane using castor plants

description: This study investigated the effects of two nitrogen fertilization levels on seed and oil yield, and the biomethane production from castor husks residue. A biological pretreatment using two white rot fungi was adopted to reduce the lignin content of capsule husks and enhance biomethane production. The study aimed to highlight the potential of castor plants as energy crops using a biorefinery approach to produce biodiesel from the oil and biomethane from the residual biomass in order to reduce agricultural waste.
DOI: 10.5281/zenodo.8252414
title: A biorefinery model for the production of oil and biomethane using castor plants

description: This study investigated the effects of two nitrogen fertilization levels on seed and oil yield, and the biomethane production from castor husks residue. A biological pretreatment using two white rot fungi was adopted to reduce the lignin content of capsule husks and enhance biomethane production. The study aimed to highlight the potential of castor plants as energy crops using a biorefinery approach to produce biodiesel from the oil and biomethane from the residual biomass in order to reduce agricultural waste.