cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.2535375
title: Data and script: Community size can affect the signals of ecological drift and niche selection on biodiversity

description: Updated version of the code. Data files are the same. This is the final version of the code, associated with a manuscript published in Ecology (doi: 10.1002/ecy.3014). A preprint is also available: https://www.biorxiv.org/content/10.1101/515098v1.abstract This is a unique dataset on insect communities sampled identically in a total of 200 streams in climatically highly different regions (100 in Brazil and 100 in Finland). The sampling design included 5 streams (communities) per watershed and provided us replicates of metacommunities (watersheds). Data also include information on in-stream variables (such as current velocity (m/s), depth (cm), stream width (cm), % of sand (0.25-2 mm), gravel (2-16 mm), pebble (16-64 mm), cobble (64-256 mm), and boulder (256-1024 mm), % of canopy cover by riparian vegetation, pH, conductivity, total nitrogen, and total phosphorus) and catchment level variables (such as average slope, % of native forest cover, pasture, agriculture, planted forests, urban areas, mining, water bodies, bare soil, secondary forest cover, and mixed land uses). In addition to the dataset, here we also provide and R code used to investigate the relationship between beta diversity and community size. This code calculates 4 types of beta-diversity metric for each of 100 watersheds (5 streams) in Brazil and Finland. Beta diversity: Sorensen and Bray-Curtis dissimilarity between all pairs. Beta deviation from null models: Raup-Crick (vegan version) and Bray-Curtis beta-deviation (based on the scripts by Chris Catano and Jonathan Myers). These beta diversity metrics are modelled against community size, environmental heterogeneity and spatial extent.
description: This research originated during a joint research project funded by grant #2013/50424-1 (São Paulo Research Foundation, FAPESP) to TS, and by grants #273557 and #273560 to JH and JS (Academy of Finland).
DOI: 10.5281/zenodo.5650141
title: Accession passport and sequence data

description: Accession passport data corresponding to <em>An2-like</em> and <em>Ant1 </em>sequence data.
description: Passport data and information about sequence lenghts.
description: {"references": ["Hosmani PS, Flores-Gonzalez M, van de Geest H, et al. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. bioRxiv doi: https://doi.org/10.1101/767764", "Hulse-Kemp AM, Maheshwari S, Stoffel K, et al. 2018. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Horticulture research 5, 1-13.", "PGS Consortium. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195.", "The 100 Tomato Genome Sequencing Consortium. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant Journal 80, 136\u2013148."]}
DOI: 10.5281/zenodo.5650140
title: Accession passport and sequence data

description: Accession passport data corresponding to <em>An2-like</em> and <em>Ant1 </em>sequence data.
description: Passport data and information about sequence lenghts.
description: {"references": ["Hosmani PS, Flores-Gonzalez M, van de Geest H, et al. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. bioRxiv doi: https://doi.org/10.1101/767764", "Hulse-Kemp AM, Maheshwari S, Stoffel K, et al. 2018. Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library. Horticulture research 5, 1-13.", "PGS Consortium. 2011. Genome sequence and analysis of the tuber crop potato. Nature 475, 189-195.", "The 100 Tomato Genome Sequencing Consortium. 2014. Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant Journal 80, 136\u2013148."]}
DOI: 10.5281/zenodo.5645046
title: Seasonal Terrestrial Water Load Modulation of Seismicity at the Southeastern Margin of the Tibetan Plateau Constrained by GNSS and GRACE Data

description: Data Set S1. The earthquake catalog is used to decluster aftershocks and background events, and the time range is from July 2004 to July 2021. This data set includes 672585 events in the study area. Data Set S2. Focal mechanism solutions of M ≥ 4 earthquakes at the southeastern margin of the Tibetan Plateau. The data set includes 634 solutions of earthquakes M ≥ 4, and the time range is from 2009 to 2017.
DOI: 10.5281/zenodo.5235629
title: Seasonal Terrestrial Water Load Modulation of Seismicity at the Southeastern Margin of the Tibetan Plateau Constrained by GNSS and GRACE Data

description: Data Set S1. The earthquake catalog is used to decluster aftershocks and background events, and the time range is from July 2004 to July 2021. This data set includes 672585 events in the study area. Data Set S2. Focal mechanism solutions of M ≥ 4 earthquakes at the southeastern margin of the Tibetan Plateau. The data set includes 634 solutions of earthquakes M ≥ 4, and the time range is from 2009 to 2017.
DOI: 10.5281/zenodo.5650150
title: Summary of PCR based markers used in this study

description: Markers corresponding to the <em>atv</em>, <em>An2-like</em>, <em>Ant1</em>, <em>B</em>, and <em>u </em>loci for candidate gene development and QTL validation. Marker type and the restriction enzyme used are provided.
description: {"references": ["Orchard CJ. 2014. Naturally occurring variation in the promoter of the chromoplast-specific Cyc-B gene in tomato can be used to modulate levels of \u00df-carotene in ripe tomato fruit. Master's thesis, The Ohio State University. http://rave.ohiolink.edu/etdc/view?acc_num=osu1416926782. Accessed September 2021", "Sapir M, Oren-Shamir M, Ovadia R, Reuveni M, Evenor D, Tadmor Y, Nahon S, Shlomo H, Chen L, Meir A, Levin I. 2008. Molecular aspects of Anthocyanin fruit tomato in relation to high pigment-1. Journal of Heredity 99, 292-303."]}
DOI: 10.5281/zenodo.5650149
title: Summary of PCR based markers used in this study

description: Markers corresponding to the <em>atv</em>, <em>An2-like</em>, <em>Ant1</em>, <em>B</em>, and <em>u </em>loci for candidate gene development and QTL validation. Marker type and the restriction enzyme used are provided.
description: {"references": ["Orchard CJ. 2014. Naturally occurring variation in the promoter of the chromoplast-specific Cyc-B gene in tomato can be used to modulate levels of \u00df-carotene in ripe tomato fruit. Master's thesis, The Ohio State University. http://rave.ohiolink.edu/etdc/view?acc_num=osu1416926782. Accessed September 2021", "Sapir M, Oren-Shamir M, Ovadia R, Reuveni M, Evenor D, Tadmor Y, Nahon S, Shlomo H, Chen L, Meir A, Levin I. 2008. Molecular aspects of Anthocyanin fruit tomato in relation to high pigment-1. Journal of Heredity 99, 292-303."]}
DOI: 10.25345/c5086j
title: MassIVE MSV000088323 - Pacific Ocean metaproteomics, METZYME KM1128
title: Global metaproteomic analyses of microbial biomass from the upper water column of the Central Pacific Ocean. This dataset was used as a discovery dataset to identify peptide biomarkers for cyanobacterial populations for use in targeted metaproteomic calibrated multiple reaction monitoring (MRM) analyses published in in Saito et al., 2014 and 2015. Saito, M. A., McIlvin, M. R., Moran, D. M., Goepfert, T. J., DiTullio, G. R., Post, A. F., and Lamborg, C. H.: Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers, Science, 345, 1173-1177, 2014. Saito, M. A., Dorsk, A., Post, A. F., McIlvin, M., Rappé, M. S., DiTullio, G., and Moran, D.: Needles in the Blue Sea: Sub‐Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome, PROTEOMICS, 15, 3521-3531, 2015.
DOI: 10.5281/zenodo.5650152
title: LA1141 × OH8245 inbred backcross (IBC) single nucleotide polymorphism (SNP) markers for genetic studies

description: The LA1141 × OH8245 157 polymorphic SNP markers from an optimized tomato panel Sim et al., 2012 were used for linkage map construction in the BC<sub>2</sub>S<sub>3</sub> IBC and composite interval mapping QTL analysis. Genetic map position and physical position corresponding to Sl4.0 (Hosmani et al., 2019), and flanking sequences are provided.
description: The LA1141 x OH8245 IBC population is available upon request
description: {"references": ["Hosmani PS, Flores-Gonzalez M, van de Geest H, et al. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. bioRxiv doi: https://doi.org/10.1101/767764", "Sim SC, Durstewitz G, Plieske J, et al. 2012. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE doi.org/10.1371/journal.pone.0040563"]}
DOI: 10.5281/zenodo.5650151
title: LA1141 × OH8245 inbred backcross (IBC) single nucleotide polymorphism (SNP) markers for genetic studies

description: The LA1141 × OH8245 157 polymorphic SNP markers from an optimized tomato panel Sim et al., 2012 were used for linkage map construction in the BC<sub>2</sub>S<sub>3</sub> IBC and composite interval mapping QTL analysis. Genetic map position and physical position corresponding to Sl4.0 (Hosmani et al., 2019), and flanking sequences are provided.
description: The LA1141 x OH8245 IBC population is available upon request
description: {"references": ["Hosmani PS, Flores-Gonzalez M, van de Geest H, et al. 2019. An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps. bioRxiv doi: https://doi.org/10.1101/767764", "Sim SC, Durstewitz G, Plieske J, et al. 2012. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS ONE doi.org/10.1371/journal.pone.0040563"]}
DOI: 10.34740/kaggle/dsv/2780924
title: Covid-19 in Singapore : Latest Detailed Data
DOI: 10.5281/zenodo.5650099
title: NeST (Nested Systems in Tumor) OBO file

description: A static version of the NeST (Nested Systems in Tumor) model in OBO format. Please see https://idekerlab.ucsd.edu/nest/ for details.
DOI: 10.5281/zenodo.5650098
title: NeST (Nested Systems in Tumor) OBO file

description: A static version of the NeST (Nested Systems in Tumor) model in OBO format. Please see https://idekerlab.ucsd.edu/nest/ for details.
DOI: 10.5281/zenodo.5330673
title: Data for Finnish Dialect Detection

description: The data used in the paper "Finnish Dialect Identification: The Effect of Audio and Text". <strong>If you use the data, please cite:</strong> Hämäläinen, Mika; Alnajjar, Khalid; Partanen, Niko & Rueter, Jack (2021). Finnish Dialect Identification: The Effect of Audio and Text. In <em>Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP)</em>. The <strong>metadata.json </strong>contains the dialectal and normalized transcriptions, the length of the wav files in milliseconds, the path to the wav file, the role of the speaker and the dialect. The <strong>data.zip*</strong> files contain the wav files. They are partial zip files to make Zenodo upload easier. <strong>Code_models.zip</strong> contains the code for training the bimodal model and the final trained model presented in the paper. There is also an OpenNMT model that is the text only model described in the paper. You can use it by running: <em>python3 -m onmt.bin.translate -model nmt-model_step_100000.pt -src source_test.txt -output pred.txt -replace_unk</em> Our dataset is licensed under CC BY NC ND 4.0. Academic use only. The corpus is based on Suomenkielen näytteitä (CC BY Kotimaisten kielten keskus).
description: {"references": ["H\u00e4m\u00e4l\u00e4inen, Mika; Alnajjar, Khalid; Partanen, Niko & Rueter, Jack (Accepted).\u00a0Finnish Dialect Identification: The Effect of Audio and Text. In\u00a0Proceedings of the 2021\u00a0Conference on Empirical Methods in Natural Language Processing (EMNLP)."]}
DOI: 10.5281/zenodo.5330672
title: Data for Finnish Dialect Detection

description: The data used in the paper "Finnish Dialect Identification: The Effect of Audio and Text". <strong>If you use the data, please cite:</strong> Hämäläinen, Mika; Alnajjar, Khalid; Partanen, Niko & Rueter, Jack (2021). Finnish Dialect Identification: The Effect of Audio and Text. In <em>Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP)</em>. The <strong>metadata.json </strong>contains the dialectal and normalized transcriptions, the length of the wav files in milliseconds, the path to the wav file, the role of the speaker and the dialect. The <strong>data.zip*</strong> files contain the wav files. They are partial zip files to make Zenodo upload easier. <strong>Code_models.zip</strong> contains the code for training the bimodal model and the final trained model presented in the paper. There is also an OpenNMT model that is the text only model described in the paper. You can use it by running: <em>python3 -m onmt.bin.translate -model nmt-model_step_100000.pt -src source_test.txt -output pred.txt -replace_unk</em> Our dataset is licensed under CC BY NC ND 4.0. Academic use only. The corpus is based on Suomenkielen näytteitä (CC BY Kotimaisten kielten keskus).
description: {"references": ["H\u00e4m\u00e4l\u00e4inen, Mika; Alnajjar, Khalid; Partanen, Niko & Rueter, Jack (Accepted).\u00a0Finnish Dialect Identification: The Effect of Audio and Text. In\u00a0Proceedings of the 2021\u00a0Conference on Empirical Methods in Natural Language Processing (EMNLP)."]}
DOI: 10.5281/zenodo.5630322
title: Aggregating statistically correlated metabolic pathways into groups to improve pathway prediction outcomes

description: We included files used in hallamlab/chap
DOI: 10.5281/zenodo.3962682
title: Aggregating statistically correlated metabolic pathways into groups to improve pathway prediction outcomes

description: We included files used in hallamlab/chap
DOI: 10.4121/16930732.v1
title: Re-Organise - Game data

description: This is an anonymised data set from a game-based learning experiment performed in 2019. In the experiment, the effect of playing a business game called Re-Organise on learning about circular business model innovation was tested. The data set consists of four RDS-datafiles, containing the pre-test (prep) and post-test (iter) results of a game group and a control group of participants. In order to make the data more accessible, these RDS-files are exported to CSV-format using the R-script in the repository.
DOI: 10.6084/m9.figshare.16922791
title: GCB-data .xlsx

description: SOC dynamics with warming in alpine meadow ecosystems on the QTP.
DOI: 10.25345/c5vg37
title: MassIVE MSV000088324 - Systematic analyses of early-stage lung cancer by scRNA-seq and lipidomic reveals aberrant lipid metabolism as detection biomarkers
title: Lung cancer is the leading cause of cancer mortality and early detection is the key to improve survival. However, there are no reliable blood-based tests currently available for early-stage lung cancer diagnosis. Here, we performed single-cell RNA sequencing of early-stage lung cancer and found lipid metabolism was broadly dysregulated in different cell types and glycerophospholipid metabolism is the most significantly altered lipid metabolism-related pathway. Untargeted lipidomics were detected in an exploratory cohort of 311 participants. Through support vector machine algorithm-based and mass spectrum-based feature selection, we have identified nine lipids as the most important detection features and developed a LC-MS-based targeted assay utilizing multiple reaction monitoring. This target assay achieved 100.00% specificity on an independent validation cohort. In a hospital-based lung cancer screening cohort of 1036 participants examined by low dose CT and a prospective clinical cohort containing 109 participants, this assay reached over 90.00% sensitivity and 92.00% specificity. Accordingly, matrix-assisted laser desorption/ionization-mass spectrometry imaging assay confirmed the selected lipids were differentially expressed in early-stage lung cancer tissues in situ. Thus, this method, designated as Lung Cancer Artificial Intelligence Detector (LCAID), may be used for early detection of lung cancer or large-scale screening of high-risk populations in cancer prevention.
DOI: 10.18112/openneuro.ds003020.v1.0.1
title: An fMRI dataset during a passive natural language listening task
DOI: 10.6084/m9.figshare.16943466.v1
title: Additional file 10 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 10
DOI: 10.6084/m9.figshare.16943466
title: Additional file 10 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 10
DOI: 10.6084/m9.figshare.16943469
title: Additional file 11 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 11
DOI: 10.6084/m9.figshare.16943469.v1
title: Additional file 11 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 11
DOI: 10.6084/m9.figshare.16943472.v1
title: Additional file 12 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 12
DOI: 10.6084/m9.figshare.16943478
title: Additional file 13 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 13
DOI: 10.6084/m9.figshare.16943478.v1
title: Additional file 13 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 13
DOI: 10.6084/m9.figshare.16943481.v1
title: Additional file 14 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 14
DOI: 10.6084/m9.figshare.16943496
title: Additional file 4 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 4
DOI: 10.6084/m9.figshare.16943496.v1
title: Additional file 4 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 4
DOI: 10.6084/m9.figshare.16943499
title: Additional file 5 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 5
DOI: 10.6084/m9.figshare.16943502.v1
title: Additional file 6 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 6
DOI: 10.6084/m9.figshare.16943499.v1
title: Additional file 5 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 5
DOI: 10.6084/m9.figshare.16943502
title: Additional file 6 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 6
DOI: 10.6084/m9.figshare.16943505.v1
title: Additional file 7 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 7
DOI: 10.6084/m9.figshare.16943505
title: Additional file 7 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 7
DOI: 10.6084/m9.figshare.16943508
title: Additional file 8 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 8
DOI: 10.6084/m9.figshare.16943511
title: Additional file 9 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 9
DOI: 10.6084/m9.figshare.16943508.v1
title: Additional file 8 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 8
DOI: 10.6084/m9.figshare.16943511.v1
title: Additional file 9 of A whole genome duplication drives the genome evolution of Phytophthora betacei, a closely related species to Phytophthora infestans

description: Additional file 9
DOI: 10.6084/m9.figshare.16943524
title: Additional file 2 of The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis

description: Additional file 2: Table S2. Microsatellite genotype data based on twelve loci.
DOI: 10.6084/m9.figshare.16943527
title: Additional file 3 of The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis

description: Additional file 3: Table S3. Sample X OTU matrix with all environmental variables.
DOI: 10.6084/m9.figshare.16943524.v1
title: Additional file 2 of The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis

description: Additional file 2: Table S2. Microsatellite genotype data based on twelve loci.
DOI: 10.6084/m9.figshare.16943527.v1
title: Additional file 3 of The role of genetic diversity and arbuscular mycorrhizal fungal diversity in population recovery of the semi-natural grassland plant species Succisa pratensis

description: Additional file 3: Table S3. Sample X OTU matrix with all environmental variables.
DOI: 10.6084/m9.figshare.16943533
title: Additional file 1 of Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype

description: Additional file 1. Supplementary Table S1. Sample metadata and parameters of sequencing and alignment quality.
DOI: 10.6084/m9.figshare.16943533.v1
title: Additional file 1 of Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype

description: Additional file 1. Supplementary Table S1. Sample metadata and parameters of sequencing and alignment quality.
DOI: 10.6084/m9.figshare.16943536
title: Additional file 2 of Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype

description: Additional file 2. Supplementary Table S2. Log2 fold changes and adjusted P values of all differentially expressed genes (Benjamini‐Hochberg adjusted P‐value &lt; 0.05, log2 fold change threshold &gt; 1) in response to MOK023 and MOK124 at each time point.
DOI: 10.6084/m9.figshare.16943536.v1
title: Additional file 2 of Bovine milk somatic cell transcriptomic response to Staphylococcus aureus is dependent on strain genotype

description: Additional file 2. Supplementary Table S2. Log2 fold changes and adjusted P values of all differentially expressed genes (Benjamini‐Hochberg adjusted P‐value &lt; 0.05, log2 fold change threshold &gt; 1) in response to MOK023 and MOK124 at each time point.