cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3966921
title: TOA-Manuscript-Performance-Evaluation-Tests

description: <strong>Table of contents</strong> This repository contains the data that support the findings of the manuscript "TOA: a software package for automated functional annotation in non-model plant species". <strong>Directories:</strong> <strong>BenchmarkTranscriptomes:</strong> Fasta files with the sequences corresponding to the benchmark transcriptomes tested in the manuscript: <strong>Cnuc:</strong> <em>Cocos nucifera</em> embryos (Huang et al., 2014). <strong>Fsyl:</strong> <em>Fagus sylvatica</em> leaves (Müller, Seifert, Lübbe, Leuschner, & Finkeldey, 2017). <strong>Pcan:</strong> <em>Pinus canariensis</em> immature xylem (Chano, Collada, & Soto, 2017). <strong>GoldStandardTranscripts:</strong> transcripts fasta files of two well known gene families of proteins in <em>Arabidopsis thaliana</em> fetched from TAIR: the kinesins gene family (GS1) (Reddy & Day, 2001) and the monolignol biosynthesis gene family (GS2) (Raes et al., 2003) <strong>EnTAP:</strong> output of the six simulation tests performed with EnTAP. <strong>TOA:</strong> output of the six simulation tests performed with TOA. <strong>TRAPID:</strong> output of the three simulation tests performed with TRAPID. <strong>Trinotate:</strong> output of the three simulation tests performed with Trinotate. <br> <strong>References:</strong> Chano, V., Collada, C., & Soto, A. (2017). Transcriptomic analysis of wound xylem formation in <em>Pinus canariensis</em>. <em>BMC Plant Biology</em>, <em>17</em>(234). doi:10.1186/s12870-017-1183-3 Huang, Y. Y., Lee, C. P., Fu, J. L., Chang, B. C. H., Matzke, A. J. M., & Matzke, M. (2014). <em>De novo</em> transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. <em>G3: Genes, Genomes, Genetics</em>, <em>4</em>(11), 2147–2157. doi:10.1534/g3.114.013409 Müller, M., Seifert, S., Lübbe, T., Leuschner, C., & Finkeldey, R. (2017). <em>De novo</em> transcriptome assembly and analysis of differential gene expression in response to drought in European beech. <em>PLoS ONE</em>, <em>12</em>(9), 1–20. doi:10.1371/journal.pone.0184167 <br> <br>
description: This work was supported by the following projects: SUBERINTRO (AGL2015-67495-C2-2-R), funded by the Spanish Ministry of Economy and Competitiveness; EDGECLOUD (RTI2018-096465-B-I00), funded by the Spanish Ministry of Science, Innovation and Universities; and EDGEDATA (P2018/TCS4499) funded by the Autonomous Community of Madrid.
DOI: 10.7910/dvn/ff3dqm/1taneu
title: replication_subsamples.smcl

description: File used with "face validity.do" to produce estimates in Table 3 of the manuscript.
DOI: 10.7910/dvn/ff3dqm/67nnra
title: ratios_by_year_MS_fig6.tab

description: Average yearly EU member state delegation ratios, constraint ratios and discretion indices used to produce Figure 6.
DOI: 10.7910/dvn/ff3dqm/7uvbew
title: FranchinoYear.tab

description: Ancillary files needed to reproduce Figures 3 & 4
DOI: 10.7910/dvn/ff3dqm/nr8yyh
title: ratios_by_year_COM_fig6.tab

description: Average yearly EU Commission delegation ratios, constraint ratios and discretion indices used to produce Figure 6.
DOI: 10.7910/dvn/ff3dqm/oh9ewe
title: directive-articles.csv

description: Full text EU directives parsed into articles. GBT classifiers are applied to these and aggregated to produce Figure 6.
DOI: 10.7910/dvn/ff3dqm/pg7s8j
title: Training_Data_COM.tab

description: Data used to train the gradient boosted tree classifier to predict EU Commission delegation and constraint.
DOI: 10.7910/dvn/ff3dqm/t7mcsg
title: Training_Data_MS.tab

description: Data used to train the gradient boosted tree classifier to predict EU member state delegation and constraint.
DOI: 10.7910/dvn/ff3dqm/vz5koa
title: franchino-link.tab

description: Ancillary files needed to reproduce Figures 3 & 4
DOI: 10.25919/5dcb0a0af3523
title: Parkes observations for project P456 semester 2019OCTS_04

description: The Parkes Pulsar Timing Array (PPTA) project has three primary goals: (a) detection of gravitational waves from astronomical sources, (b) establishment of a pulsar timescale, and (c) improvement of our understanding of Solar-system dynamics. The PPTA is the oldest of three international pulsar timing groups. We have the smallest telescope and the smallest group, but the best measurements and the best results. Our bound on the strength of the incoherent gravitational wave background is the only bound which significantly constrains theoretical models. We have maintained our leading position because: we have the southern sky; we have a small but well-focussed group; we have the best-calibrated receivers; and we have been able to observe with an almost regular cadence of 15 to 20 days over a wide bandwidth. With this proposal we aim to maintain our pre-eminent position in the field. Unlike most observing proposals, this is a continuing proposal for which the observations will continue to improve bounds on ultra-low-frequency gravitational waves until they are finally detected. Continued Parkes observations will remain valuable at least until the first stage of the SKA is able to improve on our sensitivity and observing cadence. Even after the gravitational wave background is detected we will want to continue observations in support of the nascent field of gravitational wave astronomy!
DOI: 10.7910/dvn/ff3dqm/ovs1lg
title: regulation-articles.csv

description: Full text EU regulations parsed into articles. GBT classifiers are applied to these and aggregated to produce Figure 6.
DOI: 10.25345/c5b68q
title: MassIVE MSV000084575 - Erythroxylum pungens - proteomic analysis of leaves, stem and roots
title: 1234567890 1234567890 1234567890 1234567890 1234567890 1234567890 1234567890
DOI: 10.17632/m4mys9stdc.1
title: Data for: Public good production in heterogeneous groups: An experimental analysis on the relation between external return and information

description: Stata data file contains the data set used for the analyses. Stata do file includes descriptive statistics reported in the article.
DOI: 10.5281/zenodo.3539258
title: Supplementary information for samples and data used in Salazar et al. (2019)

description: Supplementary information for samples and data used in Salazar et al. (2019). <em>Gene expression changes and community turnover differentially shape the global ocean metatranscriptome</em>. https://doi.org/10.1016/j.cell.2019.10.014
description: {"references": ["Salazar et al. (2019). Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. https://doi.org/10.1016/j.cell.2019.10.014"]}
DOI: 10.5281/zenodo.3635500
title: TOA-Manuscript-Performance-Evaluation-Tests

description: <strong>Table of contents</strong> This repository contains the data that support the findings of the manuscript "TOA: a software package for automated functional annotation in non-model plant species". <strong>Directories:</strong> <strong>BenchmarkTranscriptomes:</strong> Fasta files with the sequences corresponding to the benchmark transcriptomes tested in the manuscript: <strong>Cnuc:</strong> <em>Cocos nucifera</em> embryos (Huang et al., 2014). <strong>Fsyl:</strong> <em>Fagus sylvatica</em> leaves (Müller, Seifert, Lübbe, Leuschner, & Finkeldey, 2017). <strong>Pcan:</strong> <em>Pinus canariensis</em> immature xylem (Chano, Collada, & Soto, 2017). <strong>GoldStandardTranscripts:</strong> transcripts fasta files of two well known gene families of proteins in <em>Arabidopsis thaliana</em> fetched from TAIR: the kinesins gene family (GS1) (Reddy & Day, 2001) and the monolignol biosynthesis gene family (GS2) (Raes et al., 2003) <strong>EnTAP:</strong> output of the six simulation tests performed with EnTAP. <strong>TOA:</strong> output of the six simulation tests performed with TOA. <strong>TRAPID:</strong> output of the three simulation tests performed with TRAPID. <strong>Trinotate:</strong> output of the three simulation tests performed with Trinotate. <br> <strong>References:</strong> Chano, V., Collada, C., & Soto, A. (2017). Transcriptomic analysis of wound xylem formation in <em>Pinus canariensis</em>. <em>BMC Plant Biology</em>, <em>17</em>(234). doi:10.1186/s12870-017-1183-3 Huang, Y. Y., Lee, C. P., Fu, J. L., Chang, B. C. H., Matzke, A. J. M., & Matzke, M. (2014). <em>De novo</em> transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. <em>G3: Genes, Genomes, Genetics</em>, <em>4</em>(11), 2147–2157. doi:10.1534/g3.114.013409 Müller, M., Seifert, S., Lübbe, T., Leuschner, C., & Finkeldey, R. (2017). <em>De novo</em> transcriptome assembly and analysis of differential gene expression in response to drought in European beech. <em>PLoS ONE</em>, <em>12</em>(9), 1–20. doi:10.1371/journal.pone.0184167 <br> <br>
description: This work was supported by the following projects: SUBERINTRO (AGL2015-67495-C2-2-R), funded by the Spanish Ministry of Economy and Competitiveness; EDGECLOUD (RTI2018-096465-B-I00), funded by the Spanish Ministry of Science, Innovation and Universities; and EDGEDATA (P2018/TCS4499) funded by the Autonomous Community of Madrid.
DOI: 10.17632/6sdd5bwty3.1
title: Data for Table 1 and Fig 2 in Visuomotor error augmentation affects medio-lateral head and trunk stabilization during walking

description: 1. Each subject's data for Table 1. In Table 1, there are 4 sheets. Sheet 1 is named as “step width (cm),” and it is each subjects’ data for SW. Sheet 2 is named as “step length (cm),” and it is each subjects’ data for SL. Sheet 3 is named as “step width SD (cm),” and it is each subjects’ data for SWV. Sheet 4 is named as “step length SD (cm),” and it is each subjects’ data for SLV. 2. Each subject's data for Figure 4 and 5. 3. “C7MLnormal.mat” is the C7’s medio-lateral position in Fig. 2 under normal condition (1 min long) sampled at 100 Hz for each subject. 4. “C7MLpositive50.mat” is the C7’s medio-lateral position in Fig. 2 under +5.0 gain sampled at 100 Hz for each subject. 5. “C7MLpositive25.mat” is the C7’s medio-lateral position in Fig. 2 under +2.5 gain sampled at 100 Hz for each subject. 6. “C7MLnegative50.mat” is the C7’s medio-lateral position in Fig. 2 under -5.0 gain sampled at 100 Hz for each subject. 7. “C7MLnegative25.mat” is the C7’s medio-lateral position in Fig. 2 under -2.5 gain sampled at 100 Hz for each subject. For data in "C7MLpositive50.mat", “C7MLpositive25.mat”, “C7MLnegative50.mat” or “C7MLnegative25.mat”, each trial is 11-min long. Error augmentation started from the 1st data and last for 10 min. The last one min is post-adaptation.
DOI: 10.25387/g3.10257524
title: Supplemental Material for Kim et al., 2019

description: Supplementary figure and movie
DOI: 10.25345/c5g098
title: MassIVE MSV000084574 - GNPS - heterologous production of acylhomoserine lactones from orphaned AHL synthases from myxobacteria
title: Analysis of Archangium gephyra and 2 heterologous strains of E. coli expressing AHLs synthases AgpI and VitI. Control samples include E. coli strain and E. coli strain + empty expression plasmid pET28b. We determine myxobacterial AHL synthases produce acylhomoserine lactones C8-AHL and C9-AHL when heterologously expressed. No AHL metabolites observed in A. gephyra extracts.
DOI: 10.25387/g3.10257524.v1
title: Supplemental Material for Kim et al., 2019

description: Supplementary figure and movie
DOI: 10.5281/zenodo.3539588
title: Self medication among university students in san jose, costa rica databases

description: These is the database used for the research study "Self medication among university students in San Jose, Costa Rica". There are two csv files, a codified database and a database with legends. Please note legends are in Spanish. If you have any questions, contact natalianorori@gmail.com
DOI: 10.5281/zenodo.3539589
title: Self medication among university students in san jose, costa rica databases

description: These is the database used for the research study "Self medication among university students in San Jose, Costa Rica". There are two csv files, a codified database and a database with legends. Please note legends are in Spanish. If you have any questions, contact natalianorori@gmail.com
DOI: 10.5281/zenodo.3539374
title: ANI-1 (QCArchive View Formatted)

description: Data curated by the QCArchive team, originally sourced from github.com/isayev/ANI1_dataset. Off-equilibrium conformations and energies of 57,462 organic molecules with up to 8 heavy atoms. Molecules are sampled from the GDB-11 dataset. Configurations are generated with normal mode sampling, evaluated at the ωB97x/6–31G(d) level of theory. All molecules are neutral singlets. For more information, see http://qcarchive.molssi.org/apps/ml_datasets/.
description: {"references": ["Smith, J. S.; Isayev, O. & Roitberg, A. E. ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost. Chem. Sci., 2017, 8, 3192-3203. https://pubs.rsc.org/en/content/articlelanding/2017/sc/c6sc05720a", "Smith, J. S.; Isayev, O. & Roitberg, A. E. ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules Scientific data, 2017, 4, 170193. https://www.nature.com/articles/sdata2017193"]}
DOI: 10.5281/zenodo.3539375
title: ANI-1 (QCArchive View Formatted)

description: Data curated by the QCArchive team, originally sourced from github.com/isayev/ANI1_dataset. For more information, see http://qcarchive.molssi.org/apps/TODO.
DOI: 10.5519/qd.w5v3gxv6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (58 records)
DOI: 10.5519/qd.q4w9h7kx
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (4205 records)
DOI: 10.6073/pasta/f745cea488d1e13309a7b014d9f7bc71
title: CBH01 Konza Prairie Bison Herd Information

description: This study is to monitor Long-term changes in individual animal mass. Dataset contains combined weight information of the entire Konza Prairie bison herd. In addition, a historical version of the data is hosted which reflects an experimental division of the herd in the years covered.
DOI: 10.7910/dvn/3zfkfs/dkhywi
title: KilhefferDeerData.tab

description: Data Collected for Report Entitled ''Evaluating Legacy Effects of Hyperabundant White-Tailed Deer in Forested Stands of Harriman and Bear Mountain State Parks, New York
DOI: 10.5063/f1891459
title: Sockeye salmon brood tables, northeastern Pacific, 1922-2016

description: Brood tables, also called run reconstructions, utilize annual estimates of the total run (commercial catch plus escapement), and samples of ages, to estimate the number of recruits per age class. These data are useful for salmon biologists to understand salmon productivity and salmon life histories. These data can come in a number of different formats, but generally follow the pattern of: rows for each brood year, and columns for the estimated number of fish in each age class. This dataset consists of reformated and merged brood tables from Alaska, British Columbia, and Washington. These datasets were gathered as part of the State of Alaskan Salmon and People project (https://alaskasalmonandpeople.org/). Source information for the datasets can be found in the SourceInfo.csv file. A description of the merging and quality assurance process can be found in the broodTableProcessing.html file. Productivity (R/S) should not be directly compared among the stocks because some escapement counts are indices. Age classes are given in European Notation, where the first number is the number of winters spent in freshwater before going to sea (1 winter in freshwater = age-1.X), and the second number is the number of winters spent at se (3 winters at sea = age-X.3).
DOI: 10.5281/zenodo.3539581
title: High-resolution ptychotomography dataset of nanoporous glass

description: This repository contains nanoporous glass tomography dataset, acquired at the cSAXS beamline at the Swiss Light Source at the Paul Scherrer Institute in Villigen (Switzerland). Details about the data acquisition can be found in Ref. [1]. <strong>Citation and acknowledgements</strong> For use of the ptychographic X-ray computed tomography dataset on nanoporous glass: <em>[1] M. Holler, A. Diaz, M. Guizar-Sicairos, P. Karvinen, E. Färm, E. Härkönen, M. Ritala, A. Menzel, J. Raabe and O. Bunk. Scientific Reports, 4, 3857 (2014).</em> Alignment and tomographic reconstruction provided in "<em>aligned_phase_sinogram" and "tomogram_delta" </em> were performed by a method described in <em>[2] M. Odstrcil, M. Holler, J. Holler, M. Guizar-Sicairos,"Alignment methods for nanotomography with deep sub-pixel accuracy", Opt. Express, (2019).</em> <strong>Dataset description</strong> The provided dataset is saved in Matlab MAT v7.3 format. <em>stack_object</em> - complex valued unaligned projections with dimensions [Npix_vertical, Npix_horizontal, number_of_angles] <em>rotation_angle</em> - vector of corresponding projection angles in degrees <em>lambda</em> - wavelength of the illumination beam [m] <em>pixel_size</em> - size of the reconstruction pixel [m] <em>probe_size</em> - size of the reconstruction probe in pixels <em>aligned_phase_sinogram</em> - aligned and unwrapped phase projections <em>tomogram_delta</em> - reconstructed tomogram of real part of refractive index delta, n = 1-delta-i*beta
description: {"references": ["Holler, Mirko, et al. \"X-ray ptychographic computed tomography at 16 nm isotropic 3D resolution.\" Scientific reports 4 (2014): 3857."]}
DOI: 10.7910/dvn/7uhr1u/4u7ios
title: Cliffordetal2019_METADATA_InstrumentSpecifications.txt

description: :unav
DOI: 10.26300/jq66-eb95
title: Systematic reviews on interventions for corneal disease: What is the reliability of the evidence?
DOI: 10.7910/dvn/7uhr1u/bnklrz
title: Cliffordetal2019_Fig3.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/hekteq
title: Cliffordetal2019_Fig5b.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/hfamkj
title: Cliffordetal2019_Fig4.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/m5ntbv
title: Cliffordetal2019_Fig5a.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/n1vjpx
title: Cliffordetal2019_FigS5.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/sf6nbd
title: Cliffordetal2019_Fig2.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/tv3xdt
title: Cliffordetal2019_Fig7p1.txt

description: :unav
DOI: 10.7910/dvn/7uhr1u/zibox8
title: Cliffordetal2019_Fig7p2.txt

description: :unav
DOI: 10.17632/d232b5gpbh.4
title: Data for: Selective recovery of nickel, cobalt, manganese, and lithium from industrial waste lithium-ion batteries: A proposed leaching process and kinetic analysis

description: Supplementary data.
DOI: 10.3886/e115488v1
title: Replication files for "Pareto Improvements from Lexus Lanes: The Effects of Pricing a Portion of the Lanes on Congested Highways"

description: Though economists have long advocated road pricing as an efficiency-enhancing solution to traffic congestion, it has rarely been implemented, primarily because it is thought to create losers as well as winners. This paper shows that a judiciously designed toll applied to a portion of the lanes of a highway can generate a Pareto improvement before using the revenue, a sufficient condition being that drivers with a high value of time travel at the peak of rush hour. I obtain these new theoretical results by extending a standard dynamic congestion model to reflect an important additional traffic externality: extra traffic does not simply increase travel times, but also introduces frictions that reduce throughput. The analysis draws attention to a practical policy that may help overcome the widespread opposition to road pricing.<br>
DOI: 10.5281/zenodo.3539592
title: Compilation of data used to implement floodplain DEM algorithm in the Logone Floodplain

description: This document describes the dataset that was used in the article submitted to Geophysical Research Letters by Shastry and Durand entitled "Water Surface Elevation Constraints in a Data Assimilation Scheme to Infer Floodplain Topography: A Case Study in the Logone Floodplain". The dataset is distributed as a NetCDF file containing the Digital Elevation Models at different stages of the algorithm described in the article, and a set of excel files describing the location coordinates of flood boundaries used in the study. <strong>Description of Files</strong> <strong>Excel files</strong><br> Each excel file provides the location coordinates of flood boundaries on a particular day; the date is mentioned in the file name as YYYYMMDD. Each Sheet is each excel file corresponds to a unique flooded region on the particular day. The first column corresponds to Northing and the second Easting. The coordinates are in the WGS 1984 UTM Zone 33 N coordinate system. <strong>NetCDF file</strong><br> This file contains Digital Elevation Models (DEMs) at various stages of the algorithm. The various stages are described below.<br> 1. The Prior DEM: Multi-Error-Removed Improved-Terrain (MERIT) DEM (Yamazaki et al., 2017; http://hydro.iis.u-tokyo.ac.jp/~yamadai/MERIT_DEM/) of the Logone Floodplain in Cameroon upscaled to 500 m.<br> 2. Ensemble of particle DEMs: Spatially correlated errors added to the prior DEM to produce an ensemble of 50 particles.<br> 3. Channel smoothed ensemble of particles: The elevations of the river network smoothed in the ensemble of particles in 2.<br> 4. Flood boundary smoothed ensemble of particles: The elevations along flood boundaries provided in the excel files smoothed in the ensemble mentioned in 3.<br> 5. Water surface constrained ensemble: A water surface constraint is applied to the ensemble in 4 to produce the ensemble that goes into the particle batch smoother described in the article. <strong>Reference:</strong> Yamazaki, D., Ikeshima, D., Tawatari, R., Yamaguchi, T., O’Loughlin, F., Neal, J. C., Bates, P. D. (2017). A high-accuracy map of global terrain elevations. <em>Geophysical Research Letters</em>, 44 (11), 5844–5853. doi: 10.1002/2017GL072874