cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.25387/g3.9994643.v1
title: Supplemental Material for Buscheet al., 2019

description: <b>File S1.</b> Per chromosome read coverage distribution of Dwarf Cavendish reads. <b>File S2</b>. Comparison of SNVs in the duplicated segment on the long arm of chromosome 2 to all other SNVs in the genome. The higher read coverage at variants indicates a duplication of this region. <b>File S3</b>. List of public genomic banana sequence read samples used for comparison against Dwarf Cavendish based on the DH Pahang reference. <b>File S4</b>. Coverage plots of public genomic banana sequence read samples (File S1) for comparison against Dwarf Cavendish based on the DH Pahang reference. Samples are: <i>Musa acuminata</i>, <i>Musa acuminata</i> AYP_BOSN_r1, <i>Musa acuminata </i>ssp. banksii, <i>Musa acuminata </i>ssp.<i> </i>burmannica, <i>Musa acuminata</i> Cavendish BaXiJiao, <i>Musa acuminata </i>Gros Michel, <i>Musa acuminata </i>ssp. malaccensis, <i>Musa acuminata</i> Sucrier (Pisang Mas), <i>Musa acuminata</i> Sucrier (Pisang Mas 1998-2307), <i>Musa </i><i>acuminata</i> ssp. zebrina (blood banana), <i>Musa balbisiana</i> Pisang Klutuk Wulung, <i>Musa itinerans</i>, <i>Musa schizocarpa.</i><b><br></b> <b>File S5</b>. List of selected high impact variants between Dwarf Cavendish and DH Pahang with resulting effects predicted by SnpEff.<br><b></b>
DOI: 10.25387/g3.9994643.v2
title: Supplemental Material for Busche et al., 2019

description: <b>File S1.</b> Per chromosome read coverage distribution of Dwarf Cavendish reads. <b>File S2</b>. Comparison of SNVs in the duplicated segment on the long arm of chromosome 2 to all other SNVs in the genome. The higher read coverage at variants indicates a duplication of this region. <b>File S3</b>. List of public genomic banana sequence read samples used for comparison against Dwarf Cavendish based on the DH Pahang reference. <b>File S4</b>. Coverage plots of public genomic banana sequence read samples (File S1) for comparison against Dwarf Cavendish based on the DH Pahang reference. Samples are: <i>Musa acuminata</i>, <i>Musa acuminata</i> AYP_BOSN_r1, <i>Musa acuminata </i>ssp. banksii, <i>Musa acuminata </i>ssp.<i> </i>burmannica, <i>Musa acuminata</i> Cavendish BaXiJiao, <i>Musa acuminata </i>Gros Michel, <i>Musa acuminata </i>ssp. malaccensis, <i>Musa acuminata</i> Sucrier (Pisang Mas), <i>Musa acuminata</i> Sucrier (Pisang Mas 1998-2307), <i>Musa </i><i>acuminata</i> ssp. zebrina (blood banana), <i>Musa balbisiana</i> Pisang Klutuk Wulung, <i>Musa itinerans</i>, <i>Musa schizocarpa.</i><b><br></b> <b>File S5</b>. List of selected high impact variants between Dwarf Cavendish and DH Pahang with resulting effects predicted by SnpEff.<br><b></b>
DOI: 10.25387/g3.9905279.v2
title: Supplemental Material for Pallares, Picard, and Ayroles, 2020

description: File S1 contains step-by-step instructions for the TM3’seq library preparation protocol. File S2 contains step-by-step instructions for the mRNA extraction protocol. File S3 describes how to implement UMIs in the TM3’seq standard protocol. Table S1 contains the sequences of the oligos used in the TM3’seq protocol. Figure S1 describes general mapping parameters of the RNA samples used in this manuscript. Figure S2 shows the effect of sequencing depth and amplification cycles for TM3’seq libraries. Figure S3 summarized the results of ERCC analysis of NEB and TM3’seq libraries. Figure S4 and S5 show the raw ERCC-Dashboard output of the ERCC analysis for TM3'seq and NEB, respectively.
DOI: 10.6084/m9.figshare.3761562.v1290
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25387/g3.10251044
title: Supplemental Material for Chhotaray et al., 2019

description: Supplementary sheet 1 contains details of Illumina sequencing library preparations and Bioinformatics analysis of sequencing data. Figure S1 contains the KEGG Classification annotation statistics of Mab<sup>S </sup>and Mab<sup>R</sup> whereas Figure S2 contains the COG classification annotation statistics of Mab<sup>S </sup>and Mab<sup>R</sup>. Figure S3 and Figure S4 contain the pan-genome and core genome phylogeny of 25 complete genome sequences of <i>M. abscessus </i>species respectively. Figure S5 contains gelelectrophoresis of plasmids extracted from <i>M. abscessus </i>clinical strains. Figure S6 contains the maps representing the circular visualization of insertions and deletions in Mab<sup>R</sup> (CP034191) and Mab<sup>S</sup> (CP034181). Table S1 contains the annotations and related data for linear plasmid pMabS_GZ002 gene. Table S2 contains the information about the variation in methylation sites in the genes of interest between two clinical strains of <i>M. abscessus</i>. Table S3.1, Table S3.2, and Table S3.2, contain the information about the gene content in the inserted and deleted regions (Reference vs Mab<sup>R</sup>), (Reference vs Mab<sup>S</sup>), (Mab<sup>S </sup>vs Mab<sup>R</sup>), respectively. Table S4 contains the information about the drug susceptibility of <i>M. abscessus</i> isolates.<b> </b>Table S5 contains statistics of PF data generated by Illumina sequencing. Table S6 contains the statistics of clean data after quality control. Table S7 contains the proportion of statistics of the clean data compared to PF data after quality control. Table S8 contains the genome alignment statistics of two <i>M. abscessus </i>clinical strains obtained from Illumina sequencing. Table S9 contains the raw reads statistics of two of <i>M. abscessus </i>clinical strains generated from single molecule Real-Time (SMRT) sequencing. Table S10 contains the genome assembly statistics of two <i>M. abscessus </i>clinical strains obtained from single molecule Real-Time (SMRT) sequencing. File Xls S1 contains<b> </b>result of structural variation analysis. File Xls S2 contains the information about the identified SNVs, each motif’s methylation site, methylation score, type of methylation, and all locations of discovered motifs in strains, motif information of pMabS_GZ002 plasmid, identified methyltransferase in both strains. File Xls S3 contains the statistics of the 25 available complete genomes of <i>M. abscessus </i>used for pan-genome analysis. File Xls S4 contains the statistics number of accessory genes, unique genes as well as exclusively absent genes determined among the <i>M. abscessus </i>species. MabS.h5 and MabR.h5 contain the raw files of methylome analysis of Mab<sup>S </sup>and MabR.h5, respectively.
DOI: 10.25387/g3.10251044.v1
title: Supplemental Material for Chhotaray et al., 2019

description: Supplementary sheet 1 contains details of Illumina sequencing library preparations and Bioinformatics analysis of sequencing data. Figure S1 contains the KEGG Classification annotation statistics of Mab<sup>S </sup>and Mab<sup>R</sup> whereas Figure S2 contains the COG classification annotation statistics of Mab<sup>S </sup>and Mab<sup>R</sup>. Figure S3 and Figure S4 contain the pan-genome and core genome phylogeny of 25 complete genome sequences of <i>M. abscessus </i>species respectively. Figure S5 contains gelelectrophoresis of plasmids extracted from <i>M. abscessus </i>clinical strains. Figure S6 contains the maps representing the circular visualization of insertions and deletions in Mab<sup>R</sup> (CP034191) and Mab<sup>S</sup> (CP034181). Table S1 contains the annotations and related data for linear plasmid pMabS_GZ002 gene. Table S2 contains the information about the variation in methylation sites in the genes of interest between two clinical strains of <i>M. abscessus</i>. Table S3.1, Table S3.2, and Table S3.2, contain the information about the gene content in the inserted and deleted regions (Reference vs Mab<sup>R</sup>), (Reference vs Mab<sup>S</sup>), (Mab<sup>S </sup>vs Mab<sup>R</sup>), respectively. Table S4 contains the information about the drug susceptibility of <i>M. abscessus</i> isolates.<b> </b>Table S5 contains statistics of PF data generated by Illumina sequencing. Table S6 contains the statistics of clean data after quality control. Table S7 contains the proportion of statistics of the clean data compared to PF data after quality control. Table S8 contains the genome alignment statistics of two <i>M. abscessus </i>clinical strains obtained from Illumina sequencing. Table S9 contains the raw reads statistics of two of <i>M. abscessus </i>clinical strains generated from single molecule Real-Time (SMRT) sequencing. Table S10 contains the genome assembly statistics of two <i>M. abscessus </i>clinical strains obtained from single molecule Real-Time (SMRT) sequencing. File Xls S1 contains<b> </b>result of structural variation analysis. File Xls S2 contains the information about the identified SNVs, each motif’s methylation site, methylation score, type of methylation, and all locations of discovered motifs in strains, motif information of pMabS_GZ002 plasmid, identified methyltransferase in both strains. File Xls S3 contains the statistics of the 25 available complete genomes of <i>M. abscessus </i>used for pan-genome analysis. File Xls S4 contains the statistics number of accessory genes, unique genes as well as exclusively absent genes determined among the <i>M. abscessus </i>species. MabS.h5 and MabR.h5 contain the raw files of methylome analysis of Mab<sup>S </sup>and MabR.h5, respectively.
DOI: 10.6084/m9.figshare.3761562.v1293
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.25573/data.10046189.v2
title: Dataset: Accretion rates of low intertidal salt marshes in the Pacific Northwest

description: Salt-marsh accretion rate was investigated at sites that spanned a gradient in relative rate of sea-level rise in Washington and Oregon. Mean accretion rate over all sites was 3.6 mm yr<sup>-1</sup> (95% CI = 2.4 to 4.8 mm yr<sup>-1</sup>), which exceeded present mean sea-level-rise rate (1.3 mm yr<sup>-1</sup>; sd = 0.6). However, a mean rise rate of 5.5 mm yr<sup>-1</sup> (sd = 1.9) predicted by a moderate sea-level-change scenario to occur by the year 2050 exceeds mean accretion rate. Marshes with adequate sediment input seemed to have the capacity to keep pace with an increased sea-level-rise rate. Lowest accretion rates were recorded at sites with the least sediment supply. Accretion rate showed a weak negative correlation with sediment organic matter (measured as volatile solids) and marsh standing stock. The data suggest that moderate and high rise-rate scenarios would threaten the existence of salt marshes in the region in the absence of increased sediment supply. A better understanding is required of marsh accretion and predicted rate of sea-level rise to refine predictions of the effects of sea-level rise on Pacific Northwest salt marshes.<br>
DOI: 10.5281/zenodo.3942168
title: Experimental Repository for "Learn to Relax: Integrating 0-1 Integer Linear Programming with Pseudo-Boolean Conflict-Driven Search"

description: # Learn to Relax: Integrating 0-1 Integer Linear Programming with Pseudo-Boolean Conflict-Driven Search Experimental repository. Directory structure: - binary: contains the statically compiled RoundingSat binary used for the experiments.<br> - data: contains raw .csv data files of the experiments.<br> - plots: contains the plots in the paper, as well as additional ones.
DOI: 10.25411/aru.9976640.v1
title: Studies on thermal comfort and curvature analysis, studying similar structures and functions in nature

description: The design methodology deploys digital technologies that enable designers to experiment further with complex forms through simulations, towards creating dynamic systems that adapt to different topologies, geometries, scales and environmental conditions. Furthermore, this prototypical textile is inspired both in form and function by scales in nature It consists of an adaptable skeleton, informed by the topology of the body, and aperture-components that open and close in order to achieve natural ventilation and therefore cooling towards thermal comfort, improving the environmental impact regarding the energy consumption.<br>
DOI: 10.25411/aru.9976640
title: Studies on thermal comfort and curvature analysis, studying similar structures and functions in nature

description: The design methodology deploys digital technologies that enable designers to experiment further with complex forms through simulations, towards creating dynamic systems that adapt to different topologies, geometries, scales and environmental conditions. Furthermore, this prototypical textile is inspired both in form and function by scales in nature It consists of an adaptable skeleton, informed by the topology of the body, and aperture-components that open and close in order to achieve natural ventilation and therefore cooling towards thermal comfort, improving the environmental impact regarding the energy consumption.<br>
DOI: 10.25573/data.10304303.v1
title: Monthly Rain_ACP_Horizontal.xlsx

description: Monthly summaries of the Panama Canal Authority meteorological monitoring program. These data were collected from approximately 50 stations located in the Panama Canal watershed. Information about station locations can be found in the metadata in the file.<br><br>This file has been formatted horizontally so that monthly and seasonal patterns can be easily analyzed.<br><br>Published with permission from the Panama Canal Authority.
DOI: 10.25573/data.10304306.v1
title: Monthly Rain_ACP_Vertical.xlsx

description: Monthly summaries of the Panama Canal Authority meteorological monitoring program. These data were collected from approximately 50 stations located in the Panama Canal watershed. Information about station locations can be found in the metadata in the file.<br><br>This file has been formatted vertically so that long-term trends can be easily analyzed.<br><br>Published with permission from the Panama Canal Authority.
DOI: 10.25387/g3.10277960.v1
title: Supplemental Material for Martinez et al., 2020

description: Supplemental Materials for Martinez et al., 2018 includes:Figures S1-S4File S1File S2Reagent TableTable S1
DOI: 10.25387/g3.10301855
title: Supplemental Material for Parker et al., 2020

description: The breeds of domestic dog, Canis lupus familiaris, display a range of coat types with variation in color, texture, length, curl, and growth pattern. One trait of interest is that of partial or full hairlessness, which is found in a small number of breeds. While the standard for some breeds, such as the Xoloitzcuintli, requires sparse hair on their extremities, others are entirely bald, including the American Hairless Terrier. We identified a small, rare family of Scottish Deerhounds in which coated parents produced a mixed litter of coated and hairless offspring. To identify the underlying variant, we performed whole genome sequencing of the dam and five offspring, comparing single nucleotide polymorphisms and small insertions/deletions against an established catalog of 91 million canine variants. Of 325 homozygous alternative alleles found in both hairless dogs, 56 displayed the expected pattern of segregation and only a single, high impact variant within a coding region was observed: a single base pair insertion in exon two of SGK3 leading to a potential frameshift, thus verifying recently published findings. In addition, we observed that gene expression levels between coated and hairless dogs are similar, suggesting a mechanism other than non-sense mediated decay is responsible for the phenotype.
DOI: 10.25387/g3.10301855.v1
title: Supplemental Material for Parker et al., 2020

description: The breeds of domestic dog, Canis lupus familiaris, display a range of coat types with variation in color, texture, length, curl, and growth pattern. One trait of interest is that of partial or full hairlessness, which is found in a small number of breeds. While the standard for some breeds, such as the Xoloitzcuintli, requires sparse hair on their extremities, others are entirely bald, including the American Hairless Terrier. We identified a small, rare family of Scottish Deerhounds in which coated parents produced a mixed litter of coated and hairless offspring. To identify the underlying variant, we performed whole genome sequencing of the dam and five offspring, comparing single nucleotide polymorphisms and small insertions/deletions against an established catalog of 91 million canine variants. Of 325 homozygous alternative alleles found in both hairless dogs, 56 displayed the expected pattern of segregation and only a single, high impact variant within a coding region was observed: a single base pair insertion in exon two of SGK3 leading to a potential frameshift, thus verifying recently published findings. In addition, we observed that gene expression levels between coated and hairless dogs are similar, suggesting a mechanism other than non-sense mediated decay is responsible for the phenotype.
DOI: 10.25387/g3.10277960
title: Supplemental Material for Martinez et al., 2020

description: Supplemental Materials for Martinez et al., 2018 includes:Figures S1-S4File S1File S2Reagent TableTable S1
DOI: 10.6084/m9.figshare.3761562.v1294
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.6084/m9.figshare.9133835.v3
title: Memory and pedagogy of Gurbāṇī Saṅgīta: An autoethnographic Udāsī<sup>*</sup>

description: In 1989, I began an undertaking to revive the nearly-extinct Gurbāṇī Saṅgīta tradition, the centuries-old Gur-Sikh heritage. I located <i>vidyādhārīs</i> (knowledgeable memory bearers) who remembered original rāga forms and <i>śabadrītas</i> (Gurbāṇī compositions), knew how to play or make musical instruments that had all but vanished, and were versed in the exegetical attendance of Srī Gurū Granth Sāhib, the scriptural Gurū of the GurSikh Panth. Carefully sifting through the memory of the last remaining elders I could track, I started by harnessing everything that I could – irrespective of their familial or musical lineages. In this paper, I take stock of and analyse the <i>kalāmī</i> (written), <i>tantrī</i> (audio-visual) and, <i>zubānī</i> (memorised) assets that I was able to recover through my fieldwork across South Asia and beyond, including compositions, notations, stories, and pedagogical processes. In my judgement, it is impossible to understand the music of early modern India, including dhurpada and mridaṅga/pakhāwaj, without careful study of the Gurbāṇī Saṅgīta tradition and the riches it has transmitted to the present.
DOI: 10.25387/g3.10255844
title: Supplemental Material for Mollinari et al., 2020

description: This Supporting Information contains five files:<br><br>1. Extended Material and Methods.pdf: Detailed description of the material and methods used in the manuscript<br><br>2. S1 File.pdf: Reference genome assisted map improvement Figures and Likelihood tables<br><br>3. S2 File.xlsx: Final genetic map containing marker names, linkage groups, position, parental phase information, and position in two diploid reference genomes.<br><br>4. Supplemental_Figures.pdf: Supplemental Figures S1 Fig. to S13 Fig.<br><br>5. Supplemental_Tables.pdf: Supplemental Figures S1 Table to S5 Table<br><br>6. myGBSGenos_trifida_mergedSNPs_mergedTaxa_ch1 to 15: Raw VCF files with SNPs anchored in I. trifida reference genome.<br><br>7. myGBSGenos_triloba_mergedSNPs_mergedTaxa_ch1 to 15: Raw VCF files with SNPs anchored in I. triloba reference genome.
DOI: 10.25387/g3.10255844.v1
title: Supplemental Material for Mollinari et al., 2020

description: This Supporting Information contains five files:<br><br>1. Extended Material and Methods.pdf: Detailed description of the material and methods used in the manuscript<br><br>2. S1 File.pdf: Reference genome assisted map improvement Figures and Likelihood tables<br><br>3. S2 File.xlsx: Final genetic map containing marker names, linkage groups, position, parental phase information, and position in two diploid reference genomes.<br><br>4. Supplemental_Figures.pdf: Supplemental Figures S1 Fig. to S13 Fig.<br><br>5. Supplemental_Tables.pdf: Supplemental Figures S1 Table to S5 Table<br><br>6. myGBSGenos_trifida_mergedSNPs_mergedTaxa_ch1 to 15: Raw VCF files with SNPs anchored in I. trifida reference genome.<br><br>7. myGBSGenos_triloba_mergedSNPs_mergedTaxa_ch1 to 15: Raw VCF files with SNPs anchored in I. triloba reference genome.
DOI: 10.25411/aru.9976640.v2
title: Studies on thermal comfort and curvature analysis, studying similar structures and functions in nature

description: The design methodology deploys digital technologies that enable designers to experiment further with complex forms through simulations, towards creating dynamic systems that adapt to different topologies, geometries, scales and environmental conditions. Furthermore, this prototypical textile is inspired both in form and function by scales in nature It consists of an adaptable skeleton, informed by the topology of the body, and aperture-components that open and close in order to achieve natural ventilation and therefore cooling towards thermal comfort, improving the environmental impact regarding the energy consumption.<br>
DOI: 10.6084/m9.figshare.3761562.v1295
title: Online Labour Index: Measuring the Online Gig Economy for Policy and Research

description: Data repository for the data underlying the Online Labour Index. See http://ilabour.oii.ox.ac.uk online-labour-index/ for details.
DOI: 10.15785/sbgrid/736
title: X-Ray Diffraction data from Bacterial NlpC/P60 endopeptidase, source of 6SQX structure

description: X-Ray Diffraction data from Photobacterium damselae subsp. piscicida NlpC/P60 endopeptidase, source of 6SQX structure
DOI: 10.6084/m9.figshare.9122135.v5
title: Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups

description: Data used for the network analyses published in PLOS ONE paper ‘Understanding the intricacy of canid social systems: Structure and temporal stability of red fox (Vulpes vulpes) groups'.<br>associations_by_territory.zip: dataset for network construction and analysis of social differentiation, lagged association rate and lagged identification rates in SOCPROG. Comprises associations and animal attributes, arranged in dyadic format suitable for the construction of association matrices in SOCPROG. Self-associations are used for patch visits whern foxes were alone. Associations are separated by territory into tabs within the Excel document.<br>associations_by_season_and_year.zip: dataset of associations and attributes. Associations are split into tabs by season and year, and used to detect communities. <br><br>all_territories_pooled_for_spaceuse_network.zip: dataset of associations and attributes. Associations are based on shared space and not necessarily time. Associations from all territories and seasons are pooled into a single dataset that was used to construct space-use networks.<br>spatial_profiles.zip: patch utilisation by individual and patch within detected communities, used to construct spatial profile plots in the paper.<br>Distributions of N days observed.csv: sighting frequency distribution used for Fig A in S1 Appendix.
DOI: 10.6084/m9.figshare.10318823.v2
title: Panel Discussion: Who's afraid of data misuse? #SciData19

description: Grace Baynes chairs the panel discussion entitled 'Who's afraid of data misuse?' at Better Science through Better Data 2019 (#SciData19). <br>The panelists are:<br>- Yves-Alexandre de Montjoye, Imperial College London- Sabina Leonelli, University of Exeter- Shelley Stall, American Geophysical Union<br>he video recording, presentation slides and live scribe illustrations are included.<br><br>
DOI: 10.25386/genetics.10247969
title: Supplemental Material for Bhardwaj, Pandey, and Babu, 2020

description: Supplemental files and movies. <br>