cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7361822
title: Code & Data for "Adoption of Transparency and Openness Promotion (TOP) guidelines across journals"

description: This entry contains code and data that was used in the publication: "Adoption of Transparency and Openness Promotion (TOP) guidelines across journals" submitted in Publications journal. *It was version 2 when we added Fig_3_Tab2_Defining_science_disciplines_plus_plot.R script to version 1. *It was version 3 because we added script that calculates median and mean values of the stringency levels to version 2 data. *Latest version is version 4: we added supplementary data. #IDEA: This project was about analyzing policies of two thousand journals within the framework of eight TOP standards: <br> data citation, transparency of data, material, code and design and analysis, replication, plan and study pre-registration, <br> and two effective interventions: “Registered reports” and “Open science badges”. # MATERIALS & METHODS<br> We downloaded the TOP Factor (v33, 2022-08-29 3:12 PM) metric from the https://osf.io/kgnva/files/osfstorage/5e13502257341901c3805317 <br> website and analyzed its content with an in-house R script (in this repo):<br> 1) SCRIPT: fig1_Analyzing_journals_policies_and_TOP_guidelines.R<br> 2) SCRIPT: Figure2a_b_TOP_impl_journal_statistist_0_1_piechart_barplot.R<br> In order to get statistics about implementation of the TOP guidelines across discipline-specific journals, <br> we extracted information about journal’s disciplines from the Scopus content database. <br> We downloaded SCOPUS content coverage from the https://www.elsevier.com/solutions/scopus/how-scopus-works/content?dgcid=RN_AGCM_Sourced_300005030 (existJuly2022.xlsx)<br> and used the first Sheet.<br> We identified match between those 2 tables: <br> 3) SCRIPT: Rscript_overlapping_TOP_dataframe_and_SCOPUS_db.R<br> And resulted in Overlap_SCOPUS_TOP.rds file<br> And performed visualization and statistics:<br> 4) SCRIPT: Fig_3_Tab2_Defining_science_disciplines_plus_plot.R #RESULTS Submitted to Publications 30.9.2022. Reviewed 2.11.2022. Latest version: 25.11.2022.
DOI: 10.6084/m9.figshare.21622355.v1
title: Additional file 1 of Social return on investment economic evaluation of supportive care for lung cancer patients in acute care settings in Australia

description: Additional file 1.
DOI: 10.6084/m9.figshare.21622346.v1
title: Additional file 2 of The Revised Identification of Seniors At Risk screening tool predicts readmission in older hospitalized patients: a cohort study

description: Additional file 2. Performance criteria for two different versions of ISAR-R tool;30 and 90 days readmission outcomes (n=386)
DOI: 10.6084/m9.figshare.21622188.v1
title: Additional file 3 of The genetic and biochemical determinants of mRNA degradation rates in mammals

description: Additional file 3: Table S2. Matrices of filtered, transformed, imputed, and quantile-normalized human and mouse half-lives collected for each sample, provided along with the corresponding Ensembl gene IDs and gene names. Also provided are the aggregated half-lives for each species, computed as PC1 of each matrix.
DOI: 10.6084/m9.figshare.21622185.v1
title: Additional file 2 of The genetic and biochemical determinants of mRNA degradation rates in mammals

description: Additional file 2: Table S1. Sparse matrices of human and mouse half-lives collected for each sample, provided along with the corresponding Ensembl gene IDs and gene names. Missing values exist for mRNAs whose half-lives were not measured or provided.
DOI: 10.6084/m9.figshare.21622173.v1
title: Additional file 8 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 8. Table S6. Detected head and tail sequence of TE and kinds of TSD in OsCmt3a-1 (SRR1610772) and OsCmt3a-2 (SRR1609962) by Junction method.
DOI: 10.6084/m9.figshare.21622167.v1
title: Additional file 6 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 6. Table S4. Detected head and tail sequence of TE and their inserted positions on the reference sequence for hc4 and hc31 by TSD method.
DOI: 10.6084/m9.figshare.21622161.v1
title: Additional file 4 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 4. Table S2. Detected head and tail sequence of TE and kinds of TSD in ttm2 and ttm5 by TSD method.
DOI: 10.6084/m9.figshare.21622158.v1
title: Additional file 3 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 3. Table S1. Detected head and tail sequence of TE and their inserted positions on the reference sequence by TSD method.
DOI: 10.6084/m9.figshare.21622146.v1
title: Additional file 16 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 16. Table S14. Detected head and tail sequence of TE and their inserted positions on the reference sequence for SRR866312 and SRR866314 by Junction and TSD methods.
DOI: 10.6084/m9.figshare.21622143.v1
title: Additional file 15 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 15. Table S13. Detected head and tail sequence of TE and kinds of TSD in SRR823377 and SRR823382.
DOI: 10.6084/m9.figshare.21622140.v1
title: Additional file 14 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 14. Table S12. Detected head and tail sequence of TE and their inserted positions on the reference sequence for SRR823377 and SRR823382 by Junction and TSD methods.
DOI: 10.6084/m9.figshare.21622137.v1
title: Additional file 13 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 13. Table S11. Head and tail sequences of TE element among JRC lines detected by junction method. Head, tail and flanking sequences are detected by comparison between JRC lines and Nipponbare short reads. Line names of TE insertion with same flanking sequences are listed.
DOI: 10.6084/m9.figshare.21622134.v1
title: Additional file 12 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 12. Table S10. Detected head and tail sequence of TE and kinds of TSD in JRC01 and JRC05 by Junction method.
DOI: 10.6084/m9.figshare.21622131.v1
title: Additional file 11 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 11. Table S9. Detected head and tail sequence of TE and their inserted positions on the reference sequence for JRC01 and JRC05 by Junction method.
DOI: 10.6084/m9.figshare.21622128.v1
title: Additional file 10 of Transposable element finder (TEF): finding active transposable elements from next generation sequencing data

description: Additional file 10. Table S8. Detected head and tail sequence of TE and kinds of TSD in DRR001193 and DRR001194 by Junction method.
DOI: 10.6084/m9.figshare.21622074.v1
title: Additional file 3 of Effects of a small-sided games training program in youth male soccer players: variations of the locomotor profile while interacting with baseline level and with the accumulated load

description: Additional file 3. Dataset of physical fitness assessment performed in the players
DOI: 10.6084/m9.figshare.21622071.v1
title: Additional file 2 of Effects of a small-sided games training program in youth male soccer players: variations of the locomotor profile while interacting with baseline level and with the accumulated load

description: Additional file 2. Dataset of heart rate and locomotor responses during the 5v5 format
DOI: 10.6084/m9.figshare.21622068.v1
title: Additional file 1 of Effects of a small-sided games training program in youth male soccer players: variations of the locomotor profile while interacting with baseline level and with the accumulated load

description: Additional file 1. Dataset of heart rate and locomotor responses during the 3v3 format
DOI: 10.6084/m9.figshare.21622028.v1
title: Additional file 10 of Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity

description: Additional file 10: Tables S1-S36. Genomic and metabolomic raw data and analyses, metadata and primer sets used in this study.
DOI: 10.6084/m9.figshare.21622020.v1
title: Additional file 3 of Enhancement of acarbose production by genetic engineering and fed-batch fermentation strategy in Actinoplanes sp. SIPI12-34

description: Additional file 3: Table S2. Primers used in this study.
DOI: 10.6084/m9.figshare.21622017.v1
title: Additional file 2 of Enhancement of acarbose production by genetic engineering and fed-batch fermentation strategy in Actinoplanes sp. SIPI12-34

description: Additional file 2: Table S1. Strains and plasmids used in this study.
DOI: 10.5281/zenodo.7361883
title: Delirium in older hospitalized patients - a prospective analysis of the detailed course of delirium in geriatric inpatients

description: Inpatients of a geriatric ward were screened for delirium and in the case of presence of delirium included into the study. Patients received three assessments including Mini-Mental-Status-Examination (MMSE) and the Delirium Rating Scale Revised 98 (DRS-R-98).
DOI: 10.5281/zenodo.7361882
title: Delirium in older hospitalized patients - a prospective analysis of the detailed course of delirium in geriatric inpatients

description: Inpatients of a geriatric ward were screened for delirium and in the case of presence of delirium included into the study. Patients received three assessments including Mini-Mental-Status-Examination (MMSE) and the Delirium Rating Scale Revised 98 (DRS-R-98).
DOI: 10.6084/m9.figshare.21622008.v1
title: Additional file 4 of Pure somatic pathogenic variation profiles for patients with serrated polyposis syndrome: a case series

description: Additional file 4: Table S4. Mutational signature of the single base substitution.
DOI: 10.6084/m9.figshare.21622007.v1
title: Additional file 3 of A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

description: Additional file 3: SNP genotypes of woodrats sampled in Indiana, New Jersey, Ohio and Pennsylvania. The spreadsheet labeled “Raw Data” includes the genotypes for 318 individuals genotyped at 134 SNP loci.
DOI: 10.6084/m9.figshare.21622005.v1
title: Additional file 3 of Pure somatic pathogenic variation profiles for patients with serrated polyposis syndrome: a case series

description: Additional file 3: Table S3. Mutational signature of the single base substitutions (SBS).
DOI: 10.6084/m9.figshare.21622002.v1
title: Additional file 2 of Pure somatic pathogenic variation profiles for patients with serrated polyposis syndrome: a case series

description: Additional file 2: Table S2. DNA variant profile (Case #2).
DOI: 10.6084/m9.figshare.21622001.v1
title: Additional file 1 of A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

description: Additional file 1: Microsatellite genotypes of woodrats sampled in 2009, 2011 and 2012 in the Palisades, NJ. The spreadsheets labeled “Raw Data” and “data GenAlEx” include the genotypes for twenty-eight individuals genotyped at 11 microsatellite loci. These individuals had relatively low genetic variability, as indicated by number of alleles (spreadsheets AFP and AGL), observed heterozygosity and expected heterozygosity (spreadsheet HFP).
DOI: 10.6084/m9.figshare.21621999.v1
title: Additional file 1 of Pure somatic pathogenic variation profiles for patients with serrated polyposis syndrome: a case series

description: Additional file 1: Table S1. DNA variant profile (Case #1).
DOI: 10.18462/cours.mellari.insta.10.2022
title: Installations frigorifiques à compression mécanique.
DOI: 10.6084/m9.figshare.21621909.v1
title: Additional file 1 of Population genetic study of 17 Y-STR Loci of the Sorani Kurds in the Province of Sulaymaniyah, Iraq

description: Additional file 1: Table S1. Y-STR haplotypes and predicted haplogroups for 157 Iraqi [Sorani Kurd] males. Table S2. Allele frequencies and sample size by locus of the 17-STR loci for the 157 males of the Sorani Kurd. Table S3. Gene diversity (GD), polymorphism information content (PIC), match probability (PM) and power of discrimination (PD) of the Sorani Kurd males. Table S4. Haplogroup distribution in Sorani Kurdish population. Table S5. Sum of squared size difference (Rst) in 15 populations.
DOI: 10.25573/serc.21206261
title: Data for: Nitrogen addition increases freeze resistance in black mangrove (Avicennia germinans) shrubs in a temperate-tropical ecotone

description: <br> Low temperature stress is the primary factor determining the latitudinal limits of tropical plants. As the climate warms, tropical species are migrating poleward, displacing native species and modifying ecosystem structure and function. Changes are particularly evident along latitudinal gradients with the highest velocity of change occurring in wetlands. In coastal wetlands, saltmarshes dominate at latitudes above 30°, whereas mangroves occur mostly in the tropics because most species are intolerant of freezing temperatures, but others, like Avicennia germinans (black mangrove), do tolerate freezing temperatures. In response to a warmer climate and fewer killing freezes, mangroves are currently expanding into saltmarshes. However, the speed of the transition from saltmarsh to mangrove can also be modified by extreme events and nutrient subsidies. In a fertilization experiment along the Atlantic coast of North America, we found that nitrogen addition altered plant traits in Avicennia, which increased their resistance to freezing temperatures. This trait shift resulted in negligible freeze effects during a January 2018 extreme freeze event compared to unfertilized plants, which lost &gt;80% of the leaves and &gt;40% of the wood in their canopies. The freeze-killed litter from unfertilized plants provided a nutrient pulse that influenced recovery, growth and mangrove cover for three years following the freeze. Nutrient enrichment and recovery from the freeze effects led to increased growth and structural complexity of the mangrove canopy, which further enhanced freeze tolerance, shrub growth form, and the ability of Avicennia to displace the saltmarsh in the temperate-tropical ecotone.
DOI: 10.25573/serc.21206261.v1
title: Data for: Nitrogen addition increases freeze resistance in black mangrove (Avicennia germinans) shrubs in a temperate-tropical ecotone

description: <br> Low temperature stress is the primary factor determining the latitudinal limits of tropical plants. As the climate warms, tropical species are migrating poleward, displacing native species and modifying ecosystem structure and function. Changes are particularly evident along latitudinal gradients with the highest velocity of change occurring in wetlands. In coastal wetlands, saltmarshes dominate at latitudes above 30°, whereas mangroves occur mostly in the tropics because most species are intolerant of freezing temperatures, but others, like Avicennia germinans (black mangrove), do tolerate freezing temperatures. In response to a warmer climate and fewer killing freezes, mangroves are currently expanding into saltmarshes. However, the speed of the transition from saltmarsh to mangrove can also be modified by extreme events and nutrient subsidies. In a fertilization experiment along the Atlantic coast of North America, we found that nitrogen addition altered plant traits in Avicennia, which increased their resistance to freezing temperatures. This trait shift resulted in negligible freeze effects during a January 2018 extreme freeze event compared to unfertilized plants, which lost &gt;80% of the leaves and &gt;40% of the wood in their canopies. The freeze-killed litter from unfertilized plants provided a nutrient pulse that influenced recovery, growth and mangrove cover for three years following the freeze. Nutrient enrichment and recovery from the freeze effects led to increased growth and structural complexity of the mangrove canopy, which further enhanced freeze tolerance, shrub growth form, and the ability of Avicennia to displace the saltmarsh in the temperate-tropical ecotone.
DOI: 10.6084/m9.figshare.21621240.v2
title: Supplementary Data for "Long-term pollution does not significantly inhibit denitrification and DNRA by adapted benthic microbial communities"

description: <strong>Title:</strong> Long-term pollution does not significantly inhibit denitrification and DNRA by adapted benthic microbial communities <br> <strong>Supplementary Information</strong> <em>Captions to supplementary data files</em> <br> Data S1 The data file shows sequence facility ids, sample names, number of read-pairs yielded after sequencing, quality trimming and merging details, number of 16S rRNA gene sequences classified against SILVA, 18S rRNA gene sequences against NCBI NT, and meagenome sequences classified with DIAMOND against the MEGAN supplied KEGG database. <br> Data S2 The data file shows the denitrification and DNRA results from the IPT experiment. <br> Data S3 The data file shows: sheet 1) KEGG classifications in the nitrogen metabolism pathway, and sheet 2) all the KEGG classifications for all pathways detected in th samples. The table shows normalized reads counts derived from the MEGAN software normalized read counts function (sub-sample to lowest sample size). <br> Data S4 The data file shows MEGAN taxonomy linked to KEGG classifications (metal related genes, Dioxin pathway, and Nitrogen metabolism pathways). The results are based on linking taxonomy and KEGG classifications having the same read name. The table shows normalized counts as counts per million (CPM) values. <br> Data S5 The data file shows the edgeR results (only results with FDR &lt; 0.05 are reported). The table shows log fold-change values based on pairwise comparisons between stations. <br> Data S6 The data file shows 16S rRNA gene sequences (sheet 1) extracted from the metagenome (using SortMeRNA) and classified against the SILVA database. The table shows raw read counts.
DOI: 10.6084/m9.figshare.21621240.v1
title: Supplementary Data for "Long-term pollution does not significantly inhibit denitrification and DNRA by adapted benthic microbial communities"

description: <strong>Title:</strong> Long-term pollution does not significantly inhibit denitrification and DNRA by adapted benthic microbial communities <br> <strong>Supplementary Information</strong> <em>Captions to supplementary data files</em> <br> Data S1 The data file shows sequence facility ids, sample names, number of read-pairs yielded after sequencing, quality trimming and merging details, number of 16S rRNA gene sequences classified against SILVA, 18S rRNA gene sequences against NCBI NT, and meagenome sequences classified with DIAMOND against the MEGAN supplied KEGG database. <br> Data S2 The data file shows the denitrification and DNRA results from the IPT experiment. <br> Data S3 The data file shows: sheet 1) KEGG classifications in the nitrogen metabolism pathway, and sheet 2) all the KEGG classifications for all pathways detected in th samples. The table shows normalized reads counts derived from the MEGAN software normalized read counts function (sub-sample to lowest sample size). <br> Data S4 The data file shows MEGAN taxonomy linked to KEGG classifications (metal related genes, Dioxin pathway, and Nitrogen metabolism pathways). The results are based on linking taxonomy and KEGG classifications having the same read name. The table shows normalized counts as counts per million (CPM) values. <br> Data S5 The data file shows the edgeR results (only results with FDR &lt; 0.05 are reported). The table shows log fold-change values based on pairwise comparisons between stations. <br> Data S6 The data file shows 16S rRNA gene sequences (sheet 1) extracted from the metagenome (using SortMeRNA) and classified against the SILVA database. The table shows raw read counts.
DOI: 10.5281/zenodo.7361913
title: Bilateral Cultural Agreements, 1935-1972: List of Included Agreements

description: This is the list of bilateral treaties included in the text corpus "Bilateral Cultural Agreements, 1935-1972," a curated text corpus composed of the texts of bilateral general cultural agreements signed between 1935 and 1972 and deposited with either the League of Nations Treaty Service (LTS) or United Nations Treaty Service (UNTS) and published by those organizations. For more information see the description of that corpus file. This selection of agreements could be identified thanks to the electronic World Treaty Index (worldtreatyindex.com), or eWTI [1]. An edited version of the portions of the eWTI related to cultural agreements is available at: zenodo.org/record/5159745. Discussion of the principles of selection behind this corpus, including a definition of "general cultural agreements," can be found in this article (B. G. Martin, "The Rise of the Cultural Treaty," <em>International History Review</em>, 2022); as well as in this log, which documents the decision-making process. The 464 agreements collected in this corpus represent almost exactly half of the total number of general cultural agreements signed between January 1935 and December 1972 (49.88% of 931). The remainder were not deposited with the League of Nations or the UN; some were published in national treaty collections. Read about the project at: benjamingmartin.com/cultintsoc. Code related to the project, including text analysis tools designed for this corpus, is available at the project's GitHub page. Please contact me with questions or suggestions: benjamin [dot] martin [at] idehist.uu.se [1] Paul Poast, Michael James Bommarito and Daniel Martin Katz, ‘The Electronic World Treaty Index: Collecting the Population of International Agreements in the 20th Century’, SSRN Scholarly Paper (Rochester, NY: Social Science Research Network, February 15, 2010), online at: http://papers.ssrn.com/abstract=2652760.
description: Work on this dataset, conducted in collaboration with Humlab (Umeå University), was supported by the Swedish Foundation for Humanities and Social Sciences (Riksbankens Jubileumsfond), P16-0900:1.