cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13853756
title: Additional scripts

description: Additional Perl scripts for the tufted duck annotation project and R scripts for visualisation of results.<br>Perl scripts:tama_merge_report_parser.pl: parse gene report of tama_merge.pytblout2gff3.pl: convert cmscan's toblout result to gff3 format<br>R scripts:ncRNA_distributions.R: exons per transcript and transcript length distributionsprotein_coding_potential.R: Venn diagram for CPC2-predicted and UniRef50 identified ORFstranscript_model_histograms.R: histograms for structural annotations per tissue and pipelineUpSetR_uniprot_supported.R: evidence for expressed genes per tissue/pipeline<br>Input files:all_counts_hisat_stringtie_threshold_ends.txt: count data for transcript_model_histograms.Rexons_per_transcripts.txt and transcript_lengths.txt: count data for ncRNA_distributions.Rgene_report_supported_by_uniprot.csv: binary TRUE or FALSE for gene report by tissue/pipeline; input for UpSetR_uniprot_supported.Rgenes_found_cpc.txt and genes_found_uniprot.txt: identified genes CPC2 and UniRef50; input for protein_coding_potential.R
DOI: 10.6084/m9.figshare.13852256
title: Illumina small RNA-Seq

description: Small RNA sequenced on Illumina platform were annotated.Illumina raw reads were quality-checked with FastQC, adapters and contamination removed with Cutadapt, quality-checked again, reads mapped to the tufted duck reference genome with STAR, transcripts assembled with Cufflinks, nucleotide sequences extracted with bedtools, small RNA predicted in the reference genome and annotated with assembled small RNA using the Infernal tool cmscan, output converted to gff3 with tblout3gff3.pl.cutadapt options: ${-m 9 -q 20 -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC}STAR options: ${--outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMheaderHD @HD VN:1.4 SO:coordinate --quantMode GeneCounts --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1}cmscan options (brain*): ${-Z 2.420214 --cut_ga --rfam --nohmmonly --tblout ncRNA_cmscan_brain.tblout --fmt 2 --clanin Rfam.clanin Rfam.cm}*Z-value depends on input data<br>
DOI: 10.6084/m9.figshare.13852802
title: Expression atlas

description: The merged dataset of the short-read and long-read structural annotations of six tissues was filtered for UniRef50 hits and an expression atlas created based on support of pipeline/tissue.The TAMA tool tama_mergy.py creates a gene report containing each features's source (pipeline, tissue). This gene report was parsed with tama_merge_report_parser.pl, filtered for UniRef50 hits and loaded in the R function UpSetR to visualise tissue-specific evidence for expressed genes.Parse gene report, prepare for UpSetR: ${tama_merge_report_parser.pl supermerge_hisat2_stringtie_and_thresholds_ends_gene_report.txt gene_report.csv}Get genes with UniRef50 hits in final annotation: ${awk 'BEGIN {FS="[\t;]"} $6 ~ /UniRef50/ {print $4}' supermerge_hisat2_stringtie_and_thresholds_ends.bed | sed 's/$/,/' | sort -u &gt; gene_support_uniprot.txt}Filter UpSetR list for UniRef50-supported entries: ${grep -Ff gene_support_uniprot.txt gene_report.csv &gt; gene_report_supported_by_uniprot.csv}<br>
DOI: 10.6084/m9.figshare.13850840
title: PacBio Iso-Seq, transcript models

description: Structural annotation/transcript models of RNA (cDNA) sequenced from six different tissues (brain, ileum, lung, ovary, spleen, testis) from the tufted duck on PacBio platform.Full-length non-chimeric (FLNC) reads were built according to PacBio's IsoSeq3 pipeline (ccs, lima, refine), fasta sequences extracted with Bamtools and poly-A tails trimmed with the TAMA tool tama_flnc_polya_cleanup.py. The FLNC reads were mapped to the tufted duck reference genome with Minimap2 and redundant transcript models collapsed with the TAMA tool tama_collapse.py.ccs options: ${--noPolish --minLength=300 --minPasses=1 --minZScore=-999 --maxDropFraction=0.8 --minPredictedAccuracy=0.8 --minSnr=4}lima options: ${--isoseq --dump-clips --no-pbi -j 4 Teloprime.fasta}refine options: ${Teloprime.fasta}Minimap2 options: ${--secondary=no -a -x splice -u f -C 5}tama_collapse.py options: ${-c 95 -x capped -a 100 -z 100}
DOI: 10.6084/m9.figshare.13850360
title: Illumina RNA-Seq, transcript models

description: Structural annotation/transcript models of RNA (cDNA) sequenced from six different tissues (brain, ileum, lung, ovary, spleen, testis) from the tufted duck on Illumina platform.Raw sequencing data was quality-checked with FastQC, adapters and contamination trimmed with Trimmomatic, quality-checked once again, mapped to the tufted duck reference genome with Hisat2, and transcript models assembled with StringTie2.Trimmomatic options: ${ILLUMINACLIP:TruSeq3-PE_rk.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36}Hisat2 options: ${--dta --rna-strandness RF}Stringtie2 options: ${--fr}
DOI: 10.5281/zenodo.5588794
title: WMT'16 Biomedical Translation Task - Scielo monolingual datasets

description: Monolingual data from Scielo for the Biomedical Translation Task in the First Conference on Machine Translation (WMT 16) (http://www.statmt.org/wmt16/biomedical-translation-task.html). It contains monolingual data for en, es, pt and fr. The documents were derived from the Scielo database (https://scielo.org/en/).
DOI: 10.5281/zenodo.5588793
title: WMT'16 Biomedical Translation Task - Scielo monolingual datasets

description: Monolingual data from Scielo for the Biomedical Translation Task in the First Conference on Machine Translation (WMT 16) (http://www.statmt.org/wmt16/biomedical-translation-task.html). It contains monolingual data for en, es, pt and fr. The documents were derived from the Scielo database (https://scielo.org/en/).
DOI: 10.25721/ktwd-x634
title: Marche pour conduire la mariée, sur l'air de "Ah les fraises et les framboises"
DOI: 10.5282/ubm/data.259
title: Public responsibility attributions for contested EU border control and financial policies

description: Supplementary material to: Tim Heinkelmann-Wild, Bernhard Zangl, Berthold Rittberger, and Lisa Kriegmair: Blame Shifting and Blame Obfuscation: The Blame Avoidance Effects of Delegation in the EU. In: European Journal of Political Research.
DOI: 10.5517/ccdc.csd.cc2584p9
title: CCDC 2003830: Experimental Crystal Structure Determination

description: Related Article: Fangzhou Yu, Xin Chen, Chunmei Li, Xinghu Wang, Kunlin Huang|2018|Guangzhou Huagong|46|36|
DOI: 10.5517/ccdc.csd.cc28ndgt
title: CCDC 2104976: Experimental Crystal Structure Determination

description: Related Article: Rhys P. King, Madeleine S. Woodward, Julian Grigg, Graeme McRobbie, William Levason, Gillian Reid|2021|Dalton Trans.|50|14400|doi:10.1039/D1DT02948G
DOI: 10.3886/e153061
title: Data for Does Diagnostic Feedback Promote Learning? Evidence from a Longitudinal Cognitive Diagnostic Assessment

description: Data for: Does Diagnostic Feedback Promote Learning? Evidence from a Longitudinal Cognitive Diagnostic AssessmentAuthors: Fang Tang & Peida Zhan2021-10-21 This memo documents the data files used in “Does Diagnostic Feedback Promote Learning? Evidence from a Longitudinal Cognitive Diagnostic Assessment” in AERA Open, 2021. The data were collected by the first author from six classes in a junior high school in China. They are not publicly available and have been anonymized. After data clearing, the data contain the Q-matrix and student item responses from three groups: “ScoreA.txt” for the diagnosis group, “ScoreB.txt” for the traditional group, and “ScoreC.txt” for the control group.
DOI: 10.3886/e153061v1
title: Data for Does Diagnostic Feedback Promote Learning? Evidence from a Longitudinal Cognitive Diagnostic Assessment

description: Data for: Does Diagnostic Feedback Promote Learning? Evidence from a Longitudinal Cognitive Diagnostic AssessmentAuthors: Fang Tang & Peida Zhan2021-10-21 This memo documents the data files used in “Does Diagnostic Feedback Promote Learning? Evidence from a Longitudinal Cognitive Diagnostic Assessment” in AERA Open, 2021. The data were collected by the first author from six classes in a junior high school in China. They are not publicly available and have been anonymized. After data clearing, the data contain the Q-matrix and student item responses from three groups: “ScoreA.txt” for the diagnosis group, “ScoreB.txt” for the traditional group, and “ScoreC.txt” for the control group.
DOI: 10.5281/zenodo.5588248
title: Optimizing Continuous Integration by Dynamic Test Selection

description: Replication package include source code and dataset.
DOI: 10.5281/zenodo.5588247
title: Optimizing Continuous Integration by Dynamic Test Selection

description: Replication package include source code and dataset.
DOI: 10.6084/m9.figshare.16843507
title: GWAS

description: Litter size (total number born, TNB) trait has a great impact on the economic success of pork production. The TNB consist of the number of piglets born alive (NBA) and dead (NBD). To clarify the genetic background of litter size, genome-wide association studies (GWAS) were undertaken in the present study.
DOI: 10.5282/ubm/data.260
title: AcrossBorders: List of samples analysed via iNAA including their provenance, period, description and ceramic macroscopic fabrics.

description: These lists contain the full information of all ceramics samples analysed via iNAA during the course of the AcrossBorders project in the New Kingdom town of Sai Island (Sudan). Provenance, period, description and ceramic macroscopic fabrics are indicated.
DOI: 10.5281/zenodo.5589052
title: Replication Package for: Patience and Comparative Development

description: This file contains the replication material for "Patience and Comparative Development" (forthcoming in Review of Economic Studies).
DOI: 10.5281/zenodo.5148722
title: Replication Package for: Patience and Comparative Development

description: This file contains the replication material for "Patience and Comparative Development" (forthcoming in Review of Economic Studies).
DOI: 10.6084/m9.figshare.16843573
title: COCONUT DB v 2021_10 fields description

description: Description of the fields in the MongoDB version of the COCONUT database (coconut.naturalproducts.net)
DOI: 10.6084/m9.figshare.16843573.v2
title: COCONUT DB v 2021_10 fields description

description: Description of the fields in the MongoDB version of the COCONUT database (coconut.naturalproducts.net)
DOI: 10.6084/m9.figshare.16843573.v1
title: COCONUT DB v 2021_10 fields description

description: Description of the fields in the MongoDB version of the COCONUT database (coconut.naturalproducts.net)
DOI: 10.4226/86/5a680f212c4f1
title: The ultra-structural organization of elastic fibres in the Annulus fibrosus of the intervertebral disc
DOI: 10.15161/oar.it/74200
title: CovidStat project data

description: This record contains the daily updated data of the CovidStat project. CovidStat is a project carried out by the CovidStat Working Group at INFN, whose creation was promoted within the Italian National Institute of Nuclear Physics with the aim of making a statistical analysis of the data provided daily by the Civil Protection on the spread of the pandemic in Italy. CovidStat data can interactively be browsed at https://covid19.infn.it.
description: The software to process this Root TTree is in the related identifier. Be sure to use the right corresponding version, based on the data in which Root TTree was generated.
DOI: 10.5522/04/16595978
title: Cell tracking reference dataset

description: Raw microscopy images and associated data used for validation of cell tracking algorithms.<br>
DOI: 10.5522/04/16595978.v1
title: Cell tracking reference dataset

description: Raw microscopy images and associated data used for validation of cell tracking algorithms.<br>
DOI: 10.5281/zenodo.5569521
title: FURTHER RANGE EXPANSION OF THE SCULPTURED RESIN BEE (MEGACHILE SCULPTURALIS) IN SERBIA AND BOSNIA & HERZEGOVINA (SUPPLEMENTARY MATERIAL)

description: <strong>Table S1.</strong> Records of <em>M. sculpturalis</em> from Serbia and Bosnia & Herzegovina during 2020, sorted chronologically. The unit record is defined as unique locality/date combination, hence, some recording sites encompass repeated recording events (being re-visited for various purposes); however, in few cases of extended observation of nesting activity, repeated reports are omitted. Source of data is abbreviated as: OR – Own Research (surveying by co-authors), or CSP – Citizen Science Project reports. Coordinates (Latitude, Longitude) are given in WGS84 system. Locations are given as broader toponyms and/or in combination with smaller units (municipalities, etc.), while coordinates were used to define the basic locality-units. Recorded by: co-authors are shown by initials, full surnames given for CSP contributors (but only initials if withheld by request). Recording context: mostly recorded on blooming <em>Styphnolobium</em> trees (49 out of 64), 7 based on nesting (but #46 includes both the nesting and observation on <em>Styphnolobium</em> within the same site), 9 were other contexts. Sex: F – female, M – males; indicates positively established sex of the observed specimens (some reports likely include both sexes, but undocumented). Sampling: number of collected specimens, followed by "p" if some included pollen.
DOI: 10.5281/zenodo.5569520
title: FURTHER RANGE EXPANSION OF THE SCULPTURED RESIN BEE (MEGACHILE SCULPTURALIS) IN SERBIA AND BOSNIA & HERZEGOVINA (SUPPLEMENTARY MATERIAL)

description: <strong>Table S1.</strong> Records of <em>M. sculpturalis</em> from Serbia and Bosnia & Herzegovina during 2020, sorted chronologically. The unit record is defined as unique locality/date combination, hence, some recording sites encompass repeated recording events (being re-visited for various purposes); however, in few cases of extended observation of nesting activity, repeated reports are omitted. Source of data is abbreviated as: OR – Own Research (surveying by co-authors), or CSP – Citizen Science Project reports. Coordinates (Latitude, Longitude) are given in WGS84 system. Locations are given as broader toponyms and/or in combination with smaller units (municipalities, etc.), while coordinates were used to define the basic locality-units. Recorded by: co-authors are shown by initials, full surnames given for CSP contributors (but only initials if withheld by request). Recording context: mostly recorded on blooming <em>Styphnolobium</em> trees (49 out of 64), 7 based on nesting (but #46 includes both the nesting and observation on <em>Styphnolobium</em> within the same site), 9 were other contexts. Sex: F – female, M – males; indicates positively established sex of the observed specimens (some reports likely include both sexes, but undocumented). Sampling: number of collected specimens, followed by "p" if some included pollen.
DOI: 10.5281/zenodo.5553319
title: BISICLES Pine Island Glacier simulations with strongly nonlinear friction

description: Model simulations of the ice sheet model BISICLES for 100 years on a set of topographies, sampled form a GP (plus BM2 and BedMachine) with m=1/8 Weertman friction law exponent. See chapter 5 of DOI: https://doi.org/10.21954/ou.ro.0001223d for more information
description: {"references": ["Wernecke, Andreas. Quantifying Century-Scale Uncertainties Of The Global Mean Sea Level Rise Contribution From The Amundsen Sea Sector, West Antarctica. Diss. The Open University, 2020."]}
DOI: 10.5281/zenodo.5553310
title: BISICLES Pine Island Glacier simulations with nonlinear friction

description: Model simulations of the ice sheet model BISICLES for 100 years on a set of topographies, sampled form a GP (plus BM2 and BedMachine) with m=1/3 Weertman friction law exponent. See chapter 5 of DOI: https://doi.org/10.21954/ou.ro.0001223d for more information
description: {"references": ["Wernecke, Andreas. Quantifying Century-Scale Uncertainties Of The Global Mean Sea Level Rise Contribution From The Amundsen Sea Sector, West Antarctica. Diss. The Open University, 2020."]}
DOI: 10.5281/zenodo.5589195
title: EDGAR-CORPUS

description: EDGAR-CORPUS: Billions of Tokens Make The World Go Round In the Proceedings of the Workshop on Economics and Natural Language Processing (ECONLP) - co-located with EMNLP 2021 We release EDGAR-CORPUS, a novel corpus comprising annual reports from all the publicly traded companies in the US spanning a period of more than 25 years. All the reports are downloaded, split into their corresponding items (sections), and provided in a clean, easy-to-use JSON format.
DOI: 10.5281/zenodo.5528489
title: EDGAR-CORPUS

description: EDGAR-CORPUS: Billions of Tokens Make The World Go Round In the Proceedings of the Workshop on Economics and Natural Language Processing (ECONLP) - co-located with EMNLP 2021 We release EDGAR-CORPUS, a novel corpus comprising annual reports from all the publicly traded companies in the US spanning a period of more than 25 years. All the reports are downloaded, split into their corresponding items (sections), and provided in a clean, easy-to-use JSON format.
DOI: 10.5281/zenodo.5578060
title: Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins"

description: Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins" The README files contain a description of all files and scripts in this repo.
DOI: 10.5281/zenodo.5578059
title: Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins"

description: Data set for "The effects of glycine to alanine mutations on the struc-ture of GPO collagen model proteins" The README files contain a description of all files and scripts in this repo.
DOI: 10.25502/6ztf-6w24/d
title: Light trap catches M. vitrata pod borer Penessoulou, Benin

description: In this project, we propose to develop and deploy climate-resilient, environmentally friendly and economically profitable integrated pest management approaches and tools - easily implementable by women and men farmers - to minimize the impact of insect pests in cowpea cropping systems in Burkina Faso, Niger and Nigeria. The project will have the following objectives: 1. Discovery objectives – Provide new knowledge on factors improving the performance of biocontrols. Assess the pest status of emerging, climate-driven insect pests, and the potential for their sustainable control. 2. Piloting objectives - Screen available or new biopesticides with potential to be commercialized by community-based groups and/or private sector operators. Validate locally-specific IPM baskets. 3. Scaling objectives – Mass releases of biocontrol agents from national rearing labs. Scale out the community-based production of neem tea-bags. 4. Capacity development objectives - Implement training and educational programs at all levels, including farmer, technician and graduate training, and short-term attachments for researchers. Achieving these objective will empower the project  i) to be able to better target mass releases of the biocontrol agents to specific agro-ecosystems, ii) to be better informed about the risks from climate-driven pests, and their mitigation strategies, iii) to have available more potent biopesticides and their mixtures which can be produced locally by community-based women and youth groups, vi) to understand the socio-economic drivers for gender-disaggregated IPM technology adoption and impact, and v) to increase the capacity of women and men cowpea farmer and national R4D partners to develop, disseminate and implement sustainable pest management approaches.
DOI: 10.6084/m9.figshare.16843639
title: Supplementary File 1.zip

description: IBP_PD630 genes mapped to FABIT_PD630 genome using increasing coverage and identity thresholds in liftoff: i) 100\% coverage and identity, ii) 95\% coverage and identity, and iii) 90\% coverage and identity. A Sequence Alignment Map (SAM) file is also provided to inspect the alignment of IBP\_PD630 genes over FABIT\_PD630 genome. <br>
DOI: 10.6084/m9.figshare.16843639.v1
title: Supplementary File 1.zip

description: IBP_PD630 genes mapped to FABIT_PD630 genome using increasing coverage and identity thresholds in liftoff: i) 100\% coverage and identity, ii) 95\% coverage and identity, and iii) 90\% coverage and identity. A Sequence Alignment Map (SAM) file is also provided to inspect the alignment of IBP\_PD630 genes over FABIT\_PD630 genome. <br>
DOI: 10.25424/cmcc/wellbeing-indicators-over-italy
title: Wellbeing Indicators using ERA5 downscaled @2.2 km over Italy
DOI: 10.6084/m9.figshare.14368460
title: HPDmobile H1 Ground Truth Data

description: Ground truth whole-house occupancy information from the home, collected over 30 days. Contains one csv file for each day. "occupied" gives the binary status of the home (0=vacant, 1=occupied), and "number" gives the estimated number of occupants at the time.
DOI: 10.6084/m9.figshare.14368463
title: HPDmobile H1 Image Data - hub RS5

description: Images from hub RS5 in one home, collected over 30 days. Images are grayscale, 32-by-32 pixels, and were taken every second.
DOI: 10.6084/m9.figshare.14368466
title: HPDmobile H1 Image Data - hub RS4

description: Images from hub RS4 in one home, collected over 30 days. Images are grayscale, 32-by-32 pixels, and were taken every second.
DOI: 10.6084/m9.figshare.14368469
title: HPDmobile H1 Image Zone Labels

description: Contains files for each hub and day with binary zone based occupancy, indicating if a human is present in the image (1) or not (0). These were automatically generated with the yoloV5 object detection algorithm (https://github.com/ultralytics/yolov5), and a subset was manually verified by a human. Overall for the home, the probability of an image labeled as occupied actually containing a human is 85%, and the probability of an image labeled as vacant not containing a person is 98%, based on the validated samples. Individual probabilities by hub vary from the whole house level, and can be found in the meta data file.
DOI: 10.6084/m9.figshare.14368457
title: HPDmobile H1 Environmental Data

description: Environmental data readings: temperature (degree C), relative humidity (rH%), indoor CO2 equivalent (ppm), total volatile organic compounds (ppb), illuminance (lux). Readings were collected every ten seconds from five different common areas inside the single family residence, for a period of 30 days. This zip folder contains csv files for each of the five hubs, for every day.
DOI: 10.6084/m9.figshare.14368457.v1
title: HPDmobile H1 Environmental Data

description: Environmental data readings: temperature (degree C), relative humidity (rH%), indoor CO2 equivalent (ppm), total volatile organic compounds (ppb), illuminance (lux). Readings were collected every ten seconds from five different common areas inside the single family residence, for a period of 30 days. This zip folder contains csv files for each of the five hubs, for every day.
DOI: 10.6084/m9.figshare.14368472
title: HPDmobile H1 Audio Data

description: Processed audio data, collected over 30 days, from 5 locations inside the home. Each ten second audio file was mean shifted, full wave rectified, and down-sampled, to remove identifying speech. The results are stored as csv files, by hub and by day.
DOI: 10.6084/m9.figshare.14368469.v1
title: HPDmobile H1 Image Zone Labels

description: Contains files for each hub and day with binary zone based occupancy, indicating if a human is present in the image (1) or not (0). These were automatically generated with the yoloV5 object detection algorithm (https://github.com/ultralytics/yolov5), and a subset was manually verified by a human. Overall for the home, the probability of an image labeled as occupied actually containing a human is 85%, and the probability of an image labeled as vacant not containing a person is 98%, based on the validated samples. Individual probabilities by hub vary from the whole house level, and can be found in the meta data file.