cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.7488/ds/2358
title: SUPERSEDED - Human, yeast and pig genomics: sequence submissions and first sequence descriptions in the literature (1980-2015)

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2589 ## This data collection is derived from two sources: 1) Submissions of DNA sequences of S. cerevisiae (yeast), Sus scrofa (pig) and Homo sapiens (human) to the European Nucleotide Archive, and 2) First description of these sequences in the scientific literature. The time range of the records is 1980-2000 (yeast), 1985-2005 (human) and 1990-2015 (pig). In total, each species has two associated datasets: 1) A .csv file documenting the PubMed ID of each article describing new sequences, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication, and 2) A .csv file documenting all institutions submitting to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. The approximate number of records is 28,000 publications and over 2 million sequence submissions. Some data about submitting institutions is not fully cleaned.
description: This item includes the following data files: pig_publications.csv PubMed ID of each article describing new sequences of Sus scrofa, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication. Time range: 1990-2015. pig_submissions.csv All institutions submitting sequences of Sus scrofa to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. Time range: 1990-2015. yeast_publications.csv PubMed ID of each article describing new sequences of S. cerevisiae, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication. Time range: 1980-2000. yeast_submissions.csv All institutions submitting sequences of S. cerevisiae to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. Time range: 1980-2000. human_publications.csv PubMed ID of each article describing new sequences of Homo sapiens, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication. Time range: 1985-2005. human_submissions.csv All institutions submitting sequences of Homo sapiens to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. Time range: 1985-2005. The data about pig, yeast and human submitting institutions is not fully cleaned.
DOI: 10.7488/ds/2482
title: Hurricane natural speech corpus - higher quality version

description: Single male native British-English talker recorded producing three speech sets (Harvard sentences, Modified Rhyme Test, news sentences) in quiet and while the talker was listening to speech-shaped noise at 84dB(A). This is a higher quality alternative (48kHz sampling rate as oppose to 16kHz) of the dataset available in: https://doi.org/10.7488/ds/140 . Note however that sentence alignment is not the same, i.e. the amount of silence in the beginning and the end of each sentence is different in each dataset.
DOI: 10.7488/ds/2449
title: Unusually complex phase of dense nitrogen at extreme conditions

description: This dataset contains DFT enthalpies (PBE and PBE+TS), Raman spectra and AIRSS search generators supporting the paper “Unusually Complex Phase of Dense Nitrogen at Extreme Conditions” published in Nature Communications.
DOI: 10.7488/ds/2252
title: Macro-socioeconomic-energy Model for Technology Pathways, 7see-GB, 2017

description: In a resource-constrained world with growing population and demand for energy, goods, and services with commensurate environmental impacts, we need to understand how these trends relate to various aspects of economic activity. 7see-GB is a computational model that links energy demand through to final economic consumption, and is used to explore decadal scenarios for the UK macroeconomy. This dataset includes the published model (*.vpm) from the source model 7see-GB, version 5-30 (14Nov17). They show how results were created for the paper “Consequences of selecting technology pathways on cumulative CO2 emissions for the UK”. The source model was developed in Vensim® (5.8b) and these published models can be viewed with the Vensim Reader, as provided with this dataset. There are instructions on how to navigate the published models and inspect variables shown in the paper. The .exe and .dmg files are free "Model Reader" executables for Windows/OSX which allow a user to run the model without buying the Vensim simulator.
DOI: 10.7488/ds/2304
title: Reliability Ensemble Averaging of ISIMIP NPP projections for 2095-2099 under RCP8.5

description: Multi-model averaging techniques provide opportunities to extract additional information from large ensembles of simulations. In particular, present-day model skill can be used to evaluate their potential performance in future climate simulations. Multi-model averaging methods have been used extensively in climate and hydrological sciences, but they have not been used to constrain projected plant productivity responses to climate change, which is a major uncertainty in earth system modelling. Here, we use three global observation-orientated estimates of current net primary productivity (NPP) to perform a reliability ensemble averaging (REA) using 30 global simulations of the 21st century change in NPP based on the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) ‘business as usual’ emissions scenario. We find that the three REAs support an increase in global NPP by the end of the 21st century (2095-2099) compared to 2001-2005, which is 2 – 3% stronger than the ensemble ISIMIP mean value of 24.2 Pg C y-1. Using REA also leads to a 45 – 68% reduction in the global uncertainty of 21st century NPP projection, which strengthens confidence in the resilience of the CO2 fertilization effect to climate change. This reduction in uncertainty is especially clear for boreal ecosystems although it may be an artefact due to the lack of representation of nutrient limitations on NPP in most models. Conversely, the large uncertainty that remains on the sign of the response of NPP in semi-arid regions points to the need for better observations and model development in these regions.
description: This dataset includes a netCDF file that stores the output of Reliability Ensemble Averaging applied to ISIMIP projections of NPP for 2095-2099 under RCP8.5 using CARDAMOM, FLUXCOM and MODIS as benchmarks for modern NPP. Corresponding analyses have been reported in the following journal article: Exbrayat, J.-F., Bloom, A. A., Falloon, P., Ito, A., Smallman, T. L., and Williams, M.: Reliability Ensemble Averaging of 21st century projections of terrestrial net primary productivity reduces global and regional uncertainties, Earth Syst. Dynam. Discuss., https://doi.org/10.5194/esd-2017-83, accepted, 2018.
DOI: 10.7488/ds/2591
title: A mini-atlas of gene expression for the domestic goat

description: The goat mini-atlas dataset includes 54 mRNA-Seq (poly-A selected) 75bp paired-end libraries from 20 tissues and 2 cell types from neonatal crossbred dairy goats. Gene level expression estimates, for the goat mini-atlas, are provided as unaveraged (S2 Dataset) and averaged across biological replicates (S3 Dataset) files. For each tissue a set of gene expression estimates, as transcripts per million (TPM), were obtained using the transcript quantification tool Kallisto.
DOI: 10.7488/ds/2327
title: The carbon chain-selective adenylation enzyme TamA: the missing link between fatty acid and pyrrole natural product biosynthesis
title: Raw data sets of mass spectra and coordinates of the 3D model

description: Data files of mass spectrometry (LC-MS) experiments in support of our publication. These .raw files require Mass Lynx Version 4.1 software to open.
DOI: 10.7488/ds/2580
title: SUPERSEDED - Genetic and epigenetic architectures of neurological protein biomarkers in the Lothian Birth Cohort 1936 - GWAS Proteins

description: ## THIS ITEM HAS BEEN REPLACED BY THE ONE WHICH CAN BE FOUND AT https://doi.org/10.7488/ds/2612 ## Data supporting the paper Hillary, R, McCartney, DL, Harris, S, Stevenson, A, Seeboth, A, Zhang, Q, Liewald, D, Evans, K, Ritchie, C, Tucker-Drob, EM, Wray, NR, Mcrae, AF, Visscher, PM, Deary, I & Marioni, R 2019, 'Genome and epigenome wide studies of neurological protein biomarkers in the Lothian Birth Cohort 1936', Nature Communications, vol. 10, 3160. https://doi.org/10.1038/s41467-019-11177-x. Specifically GWAS proteins. For seven GWAS summary files, there was an incorrect number of SNPs and the files were not formatted in line with the remaining, correct summary statistics files. The dataset has therefore been superseded - the corrected dataset is available at https://doi.org/10.7488/ds/2612 .
DOI: 10.7488/ds/2588
title: Granulation and suspension rheology: a unified treatment

description: Mixing a small amount of liquid into a powder can give rise to dry-looking granules; increasing the amount of liquid eventually produces a flowing suspension. We perform experiments on these phenomena using Spheriglass, an industrially-realistic model powder. Drawing on recent advances in understanding friction-induced shear thickening and jamming in suspensions, we offer a unified description of granulation and suspension rheology. A ‘liquid incorporation phase diagram’ explains the existence of permanent and transient granules and the increase of granule size with liquid content. Our results point to rheology-based design principles for industrial granulation.
description: The dataset comprises 4 .zip files which contain tab-delimited data for Figures 2, 3, and 4 from the main text and Figure 4 from the Supplementary Information respectively. A readme file with a description of the data relating to each figure is included inside each of the relevant .zip files.
DOI: 10.7488/ds/2506
title: Alba speech corpus

description: Single speaker read speech corpus of a Scottish accented female native English speaker (Alba). The corpus was recorded in four speaking styles: plain (normal read speech, around 4 hours of recordings), fast (speaking as fast as possible, around 20 mins), clear_c (computer directed speech, around 28 mins) and clear_h (hearing impaired directed speech, around 20mins). Audio files are sampled at 48kHz, segmented into sentences and saved in uncompressed formant (.wav). The underlying sentences are stored in separate text files (.txt).
DOI: 10.7488/ds/2354
title: The Global Environmental Stratification: A high-resolution bioclimate map of the world
title: GEnS

description: The Global Environmental Stratification (GEnS) is a statistically derived global bioclimate classification, providing a novel global spatial framework for the integration and analysis of ecological and environmental data. The dataset distinguishes 125 strata that are relatively homogeneous in bioclimatic conditions and can be aggregated into 18 environmental zones. The GEnS is available as a raster and vector spatial dataset for use with a Geographical Information System, and has a 30 arcsec resolution (equivalent to 0.86 km2 at the equator). The GEnS provides a robust spatial analytical framework for the aggregation of local observations, identification of gaps in current monitoring efforts and systematic design of complementary and new monitoring and research. The classification procedure is described in: Metzger M.J., Bunce R.G.H, Jongman R.H.G, Sayre R., Trabucco A., Zomer R. (2013). "A high-resolution bioclimate map of the world: a unifying framework for global biodiversity research and monitoring". Global Ecology and Biogeography 22: 630-638 - https://doi.org/10.1111/geb.12022
description: This dataset contains: 1) GenSv3.zip - The ESRI shapefile, ESRI grid and GeoTiff files for the global environmental stratification, as published Global Ecology and Biogeography. NOTE The data provided here are not projected, ie they have a geographic latitude-longitude coordinate system. While the grid has a colormap that displays the legend discussed in the paper, the shapefile does not have a separate legend file. 2) SourceDataGEnS.zip - GeoTiff grids of the 42 bioclimate variables that were considered for the GEnS, as described in Metzger et al. 2013, and listed in Appendix S1 of that publication. var4, var12, var36, and var37 were used to create the GEnS 3) prin_components.zip - GeoTiff files of 4 principal components components that we clustered to create the GEnS
DOI: 10.7488/ds/2270
title: Central cornea thickness Genome Wide Association Meta Analyses - Summary statistics

description: Results from the meta-analyses of genome-wide association studies for central cornea thickness in human. Corneal thinning is a common feature of rare Mendelian connective tissue disorders, such as Ehlers-Danlos syndrome (EDS), Marfan syndrome and osteogenesis imperfecta (OI), and extreme thinning is a clinical characteristic of brittle cornea syndrome . Thinner CCT is also observed in more common ocular disorders such as keratoconus, the leading cause of corneal transplants worldwide. Dataset pertaining to the publication “Cross-ancestry genome-wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases” which uses genetic variants imputed to the 1000 Genomes phase 1 reference in cohorts of European ancestry (14 cohorts,N=17,803) and Asian ancestry (5 cohorts, N=8,107) .
DOI: 10.35078/ksxb5b
title: Replication Data for: Ficha epidemiológica de localidade: Distrito: Diamantina | Município: Nova União

description: Levantamento Triatomínico com operações de campo ocorridas em Minas Gerais pela Superintendência de Campanhas de Saúde Pública (SUCAM) e FUNASA (Fundação Nacional de Saúde), no período de 1979 a 1999, objetivando a busca da presença de vetores da doença de Chagas ou de vestígios dessa presença. A partir dela são orientadas as operações com inseticida (pt) Triatomine survey with field operations carried out in Minas Gerais by the Public Health Campaigns Superintendence (SUCAM) and FUNASA (National Health Foundation), from 1979 to 1999, aiming to search for the presence of Chagas disease vectors or traces of that presence. From it, operations with insecticide are guided (en) Encuesta de triatominos con operaciones de campo realizada en Minas Gerais por la Superintendencia de Campañas de Salud Pública (SUCAM) y FUNASA (Fundación Nacional de Salud), de 1979 a 1999, con el objetivo de buscar la presencia de vectores de la enfermedad de Chagas o rastros de esa presencia. Desde ella se orientan las operaciones con insecticida (es)
DOI: 10.7488/ds/2254
title: Images - Night 18-19

description: Improvements in high-throughput phenotyping technologies are rapidly expanding the scope and capacity of plant biology studies to measure growth traits. Nevertheless, the costs of commercial phenotyping equipment and infrastructure remain prohibitively expensive for wide-scale uptake, while academic solutions can require significant local expertise. Here a low-cost methodology for plant biologists to build their own phenotyping system for quantifying growth rates and phenotypic characteristics of Arabidopsis thaliana rosettes throughout the diel cycle is presented. The group constructed an image capture system consisting of a near infra-red (NIR, 940 nm) LED panel with a mounted Raspberry PI NoIR camera and developed a MatLab-based software module (iDIEL Plant) to characterise rosette expansion. The software was able to accurately segment and characterise multiple rosettes within an image, regardless of plant arrangement or genotype, and batch process image sets. To further validate the system, wild-type Arabidopsis plants (Col-0) and two mutant lines with reduced Rubisco contents, pale leaves and slow growth phenotypes (1a3b and 1a2b) were grown on a single plant tray. Plants were imaged from 9 to 24 days after germination every 20 minutes throughout the 24 hour light-dark growth cycle (i.e. the diel cycle). The resulting dataset provided a dynamic and uninterrupted characterisation of differences in rosette growth and expansion rates over time for the three lines tested. The methodology offers a straightforward solution for setting up automated, scalable and low-cost phenotyping facilities in a wide range of lab environments that could greatly increase the processing power and scalability of Arabidopsis soil growth experiments. iDIEL Plant software and CAD files for image capture system (ICS).
DOI: 10.7488/ds/2561
title: Data supporting paper Harris et al. "Molecular genetic contributions to self-rated health"

description: Data supporting paper Harris et al. "Molecular genetic contributions to self-rated health" (International Journal of Epidemiology)
DOI: 10.7488/ds/2562
title: 'Hill_CB_2016' - Data supporting paper "Molecular genetic contributions to social deprivation and household income in UK Biobank". Current Biology (2016).

description: Data supporting paper "Molecular genetic contributions to social deprivation and household income in UK Biobank". Current Biology (2016). doi: 10.1016/j.cub.2016.09.035 ## Note re working with data ## Each of the three data files contains over seventeen million rows. Users will encounter difficulties if they attempt to view the content using Notepad++ or Microsoft Notepad. Microsoft Excel 2016 will not display all rows. These space-delimited text files contains seven columns, with a header row, which are listed in the readme file. ## Note re other copy ## The data files are identical to the files of the same name previously made available on the website of the Centre for Cognitive Ageing and Cognitive Epidemiology (CCACE) http://www.ccace.ed.ac.uk/node/335 as the zip archive "Hill_CB_2016.zip".
DOI: 10.7488/ds/2635
title: Relating production and perception of L2 tone: supplementary materials

description: This dataset contains supplementary materials to the paper "Relating the production and perception of L2 tone". It includes anonymised perception and production data (as CSV files) and R code to reproduce the figures and analyses described in the paper.
description: See README.txt.
DOI: 10.7488/ds/2424
title: Shilluk_2016_controlled_ThreeLevelVowelLength

description: The primary data in this dataset are audio recordings (wav format). They are utterances in the Shilluk language (Nilo-Saharan, South Sudan), recorded from 8 speakers, collected through controlled elicitation. The data were collected in order to investigate the phonological contrast between short, long, and overlong vowels in Shilluk. This dataset forms the basis of the paper "Three-level vowel length in Shilluk" authored by Remijsen, Ayoker, & Jørgensen which has been provisionally accepted for publication in Phonology. Apart from the primary data, the dataset includes various datatypes produced in the course of acoustic processing and analysis (TextGrid, Pitch, PitchTier, and Formant objects). The composition of the dataset is explained in the readme document.
description: See readme file included in this submission.
DOI: 10.7488/ds/2315
title: Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion

description: This dataset contains data corresponding to the figures in the main text of the manuscript "Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion" (Science Advances, 4, 4, eaao1170, 2018). Data is from experiments of bacteria on a glass surface. From movies recorded in time, we follow many individual cells in time and quantify their dynamics. Our results show that even in a clonal population (genetically identical cells), there are differences between individual cells in adhesion properties. The observations can be explained with a model, where cells have various numbers of adhesive patches. Cells with zero patches never adhere, cells with one patch adhere weakly and cells with multiple patches can adhere strongly. More details and background information on the data can be found in the manuscript and its figure captions and SI, and/or in the readme.txt file attached to this dataset.
DOI: 10.7488/ds/2492
title: Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy"

description: Dataset supporting the manuscript "High-throughput characterisation of bull semen motility using differential dynamic microscopy" published in PLOSone.
DOI: 10.7488/ds/2510
title: Code and accessories for 'Subcritical instabilities in plane Poiseuille flow of an Oldroyd-B fluid'

description: Recently, detailed experiments on visco-elastic channel flow have provided convincing evidence for a nonlinear instability scenario which we had argued for based on calculations for visco-elastic Couette flow. Motivated by these experiments we extend the previous calculations to the case of visco-elastic Poiseuille flow, using the Oldroyd-B constitutive model. Our results confirm that the subcritical instability scenario is similar for both types of flow, and that the nonlinear transition occurs for Weissenberg numbers somewhat larger than one. We provide detailed results for the convergence of our expansion and for the spatial structure of the mode that drives the instability. This also gives insight into possible similarities with the mechanism of the transition to turbulence in Newtonian pipe flow.
DOI: 10.7488/ds/2224
title: Yeast 18S rRNA DMS RNA structure probing ChemModSeq data

description: These fasta files were generated from fastq files from the Hector et al NAR 2014 ChemModSeq paper ( https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gku815 ). Included are biological triplicates of 18S DMS RNA structure probing data. The data were generated using the ChemModSeq pipeline (https://bitbucket.org/sgrann/chemmodseqpipeline). The reads from the raw fastq files were trimmed using FlexBar to remove adapters and low quality nucleotides. The sequence information present in the in-read random barcodes was used to remove PCR duplicates. Thus the data in the fasta files represent unique cDNAs. The first nucleotide in the forward (_1) read data is the reverse transcriptase drop-off point.
DOI: 10.7488/ds/2374
title: Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy (Part 2)

description: Part 2 of datasets supporting the manuscript "Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy". Abstract: We demonstrate differential dynamic microscopy and particle tracking for the characterization of the spatiotemporal behavior of active Janus colloids in terms of the intermediate scattering function (ISF). We provide an analytical solution for the ISF of the paradigmatic active Brownian particle model and find striking agreement with experimental results from the smallest length scales, where translational diffusion and self-propulsion dominate, up to the largest ones, which probe effective diffusion due to rotational Brownian motion. At intermediate length scales, characteristic oscillations resolve the crossover between directed motion to orientational relaxation and allow us to discriminate active Brownian motion from other reorientation processes, e.g., run-and-tumble motion. A direct comparison to theoretical predictions reliably yields the rotational and translational diffusion coefficients of the particles, the mean and width of their speed distribution, and the temporal evolution of these parameters.
description: Please check the file readme_part_2.txt