cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10933142.v2
title: Additional file 2 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 2. SRA accession ID for the 164 analyzed samples. For each of the 31 C. elegans early embryo cell type is reported the NCBI-SRA database accession ID of the replicates that passed the quality filters regarding whole embryo mRNA mass according to the authors [34]. 1st column contains the names of the 31 cell types, the 2nd contains the SRA ID of each replicate separated by commas.
DOI: 10.6084/m9.figshare.10933142.v1
title: MOESM2 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 2. SRA accession ID for the 164 analyzed samples. For each of the 31 C. elegans early embryo cell type is reported the NCBI-SRA database accession ID of the replicates that passed the quality filters regarding whole embryo mRNA mass according to the authors [34]. 1st column contains the names of the 31 cell types, the 2nd contains the SRA ID of each replicate separated by commas.
DOI: 10.6084/m9.figshare.10933127
title: Additional file 10 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 10. Enriched pathways associated to genes negatively correlated with TEs. 1st column contains over-represented Reactome pathways associated to genes negatively correlated with TE, evidenced by Panther tool with an FDR corrected p-value
DOI: 10.6084/m9.figshare.10933145.v2
title: Additional file 3 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 3. Raw read counts of the 163 C. elegans analyzed TE. Table containing the raw read counts measured with our pipeline. 1st column contains the names of the 163 analyzed TE. 2nd column contains the classes (DNA, LTR, LINE, RC, SINE) of the TE. Columns 3rd-166th contain the raw read counts for every sample measured with our pipeline.
DOI: 10.6084/m9.figshare.10933145.v1
title: MOESM3 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 3. Raw read counts of the 163 C. elegans analyzed TE. Table containing the raw read counts measured with our pipeline. 1st column contains the names of the 163 analyzed TE. 2nd column contains the classes (DNA, LTR, LINE, RC, SINE) of the TE. Columns 3rd-166th contain the raw read counts for every sample measured with our pipeline.
DOI: 10.6084/m9.figshare.10933127.v2
title: Additional file 10 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 10. Enriched pathways associated to genes negatively correlated with TEs. 1st column contains over-represented Reactome pathways associated to genes negatively correlated with TE, evidenced by Panther tool with an FDR corrected p-value
DOI: 10.6084/m9.figshare.10933109
title: Additional file 5 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 5:. Table containing the putatively transcribed TEs as part of annotated transcripts.
DOI: 10.6084/m9.figshare.10933127.v1
title: MOESM10 of Exploratory analysis of transposable elements expression in the C. elegans early embryo

description: Additional file 10. Enriched pathways associated to genes negatively correlated with TEs. 1st column contains over-represented Reactome pathways associated to genes negatively correlated with TE, evidenced by Panther tool with an FDR corrected p-value
DOI: 10.6084/m9.figshare.10933091
title: Additional file 3 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 3: Table containing the significant TEV-cis-eQTLs.
DOI: 10.6084/m9.figshare.10933091.v2
title: Additional file 3 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 3: Table containing the significant TEV-cis-eQTLs.
DOI: 10.6084/m9.figshare.10933109.v2
title: Additional file 5 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 5:. Table containing the putatively transcribed TEs as part of annotated transcripts.
DOI: 10.6084/m9.figshare.10933091.v1
title: MOESM3 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 3: Table containing the significant TEV-cis-eQTLs.
DOI: 10.6084/m9.figshare.10933082
title: Additional file 2 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 2: Table containing all TEVs used for the cis-eQTL analysis.
DOI: 10.6084/m9.figshare.10933109.v1
title: MOESM5 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 5:. Table containing the putatively transcribed TEs as part of annotated transcripts.
DOI: 10.6084/m9.figshare.10933076
title: Additional file 1 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 1: Table containing the tissue grouping used for assessing the loci most enriched in SNP-eQTLs for each tissue group.
DOI: 10.6084/m9.figshare.10933082.v2
title: Additional file 2 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 2: Table containing all TEVs used for the cis-eQTL analysis.
DOI: 10.6084/m9.figshare.10933076.v2
title: Additional file 1 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 1: Table containing the tissue grouping used for assessing the loci most enriched in SNP-eQTLs for each tissue group.
DOI: 10.6084/m9.figshare.10933082.v1
title: MOESM2 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 2: Table containing all TEVs used for the cis-eQTL analysis.
DOI: 10.6084/m9.figshare.10933076.v1
title: MOESM1 of Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

description: Additional file 1: Table containing the tissue grouping used for assessing the loci most enriched in SNP-eQTLs for each tissue group.
DOI: 10.6084/m9.figshare.10932962
title: Additional file 1 of ImaGene: a convolutional neural network to quantify natural selection from genomic data

description: Prediction accuracy of all tests performed in this study. In the file Additional_file_1.csv (.csv table) we report the classification task (e.g. binary or multiclass) and any specific option on data processing or learning setting along with the prediction accuracy for each tested case. (CSV 1 kb)
DOI: 10.6084/m9.figshare.10932962.v1
title: Additional file 1 of ImaGene: a convolutional neural network to quantify natural selection from genomic data

description: Prediction accuracy of all tests performed in this study. In the file Additional_file_1.csv (.csv table) we report the classification task (e.g. binary or multiclass) and any specific option on data processing or learning setting along with the prediction accuracy for each tested case. (CSV 1 kb)
DOI: 10.6084/m9.figshare.10932935
title: Additional file 1 of STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

description: Table. containing for each of the 540 isolates used in the present study the SRA sample accession number (i.e ERR016635), the species of origin, the expected ST, the total number of reads in the sample, the RAM peak (kB) and the running time (s) for each program. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.10932935.v2
title: Additional file 1 of STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

description: Table. containing for each of the 540 isolates used in the present study the SRA sample accession number (i.e ERR016635), the species of origin, the expected ST, the total number of reads in the sample, the RAM peak (kB) and the running time (s) for each program. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.10932935.v1
title: Additional file 1: of STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

description: Table. containing for each of the 540 isolates used in the present study the SRA sample accession number (i.e ERR016635), the species of origin, the expected ST, the total number of reads in the sample, the RAM peak (kB) and the running time (s) for each program. (XLSX 96 kb)
DOI: 10.6084/m9.figshare.10918463
title: target: An R Package to Predict Combined Function of Transcription Factors (manuscript data)

description: Data for reproducing the manuscript "target: An R Package to Predict Combined Function of Transcription Factors"
DOI: 10.6084/m9.figshare.10918463.v1
title: target: An R Package to Predict Combined Function of Transcription Factors (manuscript data)

description: Data for reproducing the manuscript "target: An R Package to Predict Combined Function of Transcription Factors"
DOI: 10.6084/m9.figshare.10911911
title: Zhang et al. JGR (2019).xls

description: This EXCEL dataset provides the raw data on electrical conductivity measurement of Fe-free or -bearing omphacite.
DOI: 10.6084/m9.figshare.10852073.v1
title: Main codes and data for the resonant dipole-dipole interaction in Weyl photonic crystals

description: This the main codes and data for the paper in titled "Extended Range of Dipole-Dipole Interactions in Periodically Structured Photonic Media", which published in Physical Review Letters 123, 173901 (2019).<br>
DOI: 10.6084/m9.figshare.10832687
title: Spatial modelling of cumulative human pressure in the tropical coastscape of Zanzibar, Tanzania

description: Coastal landscapes and seascapes (‘coastscapes’) are under immense anthropogenic pressures emanating from multiple human activities. We applied spatial modelling to characterise the cumulative pressures in the coastscape of Zanzibar’s main island Unguja (hereafter Zanzibar), in the western Indian Ocean. We modified the European Union’s list of the human pressures in this context, conjointly covering Zanzibar’s marine and terrestrial environments. We applied a widely accepted algorithm for modelling cumulative human pressure. Spatial data were gathered from various sources and, where primary data were absent, model results were used as proxies. We used a hexagon lattice with a resolution of 0.5 km2 to map the anthropogenic pressures within the coastscape. Five typologies of coastscape were identified. A total of 283.55 km (68.86%) of the island’s coastscape is under moderate to high anthropogenic pressure, while the remaining 128.06 km (31.14%) is under low to moderate pressure. Cumulative human pressures are highest in the urbanised coastal areas, especially Zanzibar City, and in the growth zones. Principal components analysis was used to further explore the coexistence of separate human pressures and their contributions to the cumulative human pressure. Predominant pressures within the coastscape were litter, noise, the introduction of synthetic compounds, and inputs of organic matter. We recommend the use of these results for coastal-zone management in Zanzibar and for prioritisation of the management efforts.
DOI: 10.6084/m9.figshare.10832981
title: The purse-seine fishery for small pelagic fishes off the Madeira Archipelago

description: Small pelagic fishes constitute a valuable food resource for human consumption and are also important components of marine food webs. At Madeira, a Portuguese archipelago in the eastern Atlantic, they are the target of a year-round purse-seine fishery operating mainly off the south coast of Madeira Island. Landings of this fishery are mostly composed of blue jack mackerel <i>Trachurus picturatus</i>, Atlantic chub mackerel <i>Scomber colias</i>, and small amounts of sardine <i>Sardina pilchardus</i>. A fisheries observation programme was carried out, from October 2016 to December 2017, to quantify discards and slipping. Large differences were detected in the proportion of each species present in the landings and in the gross catches. Large amounts of the caught <i>S. pilchardus</i> (76.6%), <i>S. colias</i> (42.6%) and even <i>T. picturatus</i> (14.2%) were either discarded dead or slipped. Reasons for discarding included small sizes and a low market value obtained in the first sale of these species. The fishing pattern in this region is in striking contrast with that for mainland Portugal, where <i>S. pilchardus</i> is the most valuable small pelagic species, fetching a high market price. The results of this study suggest a need for the introduction of specific measures to promote more effective utilisation of the resources.
DOI: 10.6084/m9.figshare.10832687.v2
title: Spatial modelling of cumulative human pressure in the tropical coastscape of Zanzibar, Tanzania

description: Coastal landscapes and seascapes (‘coastscapes’) are under immense anthropogenic pressures emanating from multiple human activities. We applied spatial modelling to characterise the cumulative pressures in the coastscape of Zanzibar’s main island Unguja (hereafter Zanzibar), in the western Indian Ocean. We modified the European Union’s list of the human pressures in this context, conjointly covering Zanzibar’s marine and terrestrial environments. We applied a widely accepted algorithm for modelling cumulative human pressure. Spatial data were gathered from various sources and, where primary data were absent, model results were used as proxies. We used a hexagon lattice with a resolution of 0.5 km2 to map the anthropogenic pressures within the coastscape. Five typologies of coastscape were identified. A total of 283.55 km (68.86%) of the island’s coastscape is under moderate to high anthropogenic pressure, while the remaining 128.06 km (31.14%) is under low to moderate pressure. Cumulative human pressures are highest in the urbanised coastal areas, especially Zanzibar City, and in the growth zones. Principal components analysis was used to further explore the coexistence of separate human pressures and their contributions to the cumulative human pressure. Predominant pressures within the coastscape were litter, noise, the introduction of synthetic compounds, and inputs of organic matter. We recommend the use of these results for coastal-zone management in Zanzibar and for prioritisation of the management efforts.
DOI: 10.6084/m9.figshare.10818608
title: Raw reducing sugar quantification

description: The enzyme-enriched supernatant of P. pastoris expression was incubated with CMC solution and the release of reducing sugar by the hydrolytic process was quantified in the DNS assay. The supernatant was incubated with the cellulosic substrate for up to 20 minutes. Uninoculated YPD medium and EV-transfected inoculated medium were also detected to discard residual reducing sugars present in the reaction medium and in the basal activity of other <i>P. pastoris</i> hydrolases. TlicBgluc1 activity can enrich the reaction medium in glucose equivalents approximately twice as much as the control (2.13 mM glucose to 4.76 mM glucose).
DOI: 10.6084/m9.figshare.10832981.v2
title: The purse-seine fishery for small pelagic fishes off the Madeira Archipelago

description: Small pelagic fishes constitute a valuable food resource for human consumption and are also important components of marine food webs. At Madeira, a Portuguese archipelago in the eastern Atlantic, they are the target of a year-round purse-seine fishery operating mainly off the south coast of Madeira Island. Landings of this fishery are mostly composed of blue jack mackerel <i>Trachurus picturatus</i>, Atlantic chub mackerel <i>Scomber colias</i>, and small amounts of sardine <i>Sardina pilchardus</i>. A fisheries observation programme was carried out, from October 2016 to December 2017, to quantify discards and slipping. Large differences were detected in the proportion of each species present in the landings and in the gross catches. Large amounts of the caught <i>S. pilchardus</i> (76.6%), <i>S. colias</i> (42.6%) and even <i>T. picturatus</i> (14.2%) were either discarded dead or slipped. Reasons for discarding included small sizes and a low market value obtained in the first sale of these species. The fishing pattern in this region is in striking contrast with that for mainland Portugal, where <i>S. pilchardus</i> is the most valuable small pelagic species, fetching a high market price. The results of this study suggest a need for the introduction of specific measures to promote more effective utilisation of the resources.
DOI: 10.6084/m9.figshare.10820516
title: OpenWSI

description: This dataset provides instructions on how to create an low-cost whole slide imaging prototype via single-shot autofocusing and open-source hardware.
DOI: 10.6084/m9.figshare.10818608.v1
title: Raw reducing sugar quantification

description: The enzyme-enriched supernatant of P. pastoris expression was incubated with CMC solution and the release of reducing sugar by the hydrolytic process was quantified in the DNS assay. The supernatant was incubated with the cellulosic substrate for up to 20 minutes. Uninoculated YPD medium and EV-transfected inoculated medium were also detected to discard residual reducing sugars present in the reaction medium and in the basal activity of other <i>P. pastoris</i> hydrolases. TlicBgluc1 activity can enrich the reaction medium in glucose equivalents approximately twice as much as the control (2.13 mM glucose to 4.76 mM glucose).
DOI: 10.6084/m9.figshare.10816532
title: Dataset.covars

description: The following data sets are provided to do SKAT_EMMAX test:Dataset.fam, Dataset.covars, Dataset.kinship, gene.raw, gene.gene<br>
DOI: 10.6084/m9.figshare.10816532.v1
title: Dataset.covars

description: The following data sets are provided to do SKAT_EMMAX test:Dataset.fam, Dataset.covars, Dataset.kinship, gene.raw, gene.gene<br>
DOI: 10.6084/m9.figshare.10802150
title: Raw qPCR data

description: (A) Expression of the new TlicBgluc gene was evaluated by qPCR at different stages of insect life (egg, larval stage early –ELI, late larval stage - LLI, pupa, moth) to determine the stage at which the gene exhibits higher expression. According to the results, the gene was widely expressed throughout the insect's life cycle, but expression increased significantly at the late larval stage (LLI), when the insect required most glucose utilization. (B) In the larval stage, TlicBgluc expression was evaluated in the midgut and carcass. Gene transcripts are massively detected in the gut. TlicGAPDH and TlicRPS18 were chosen as endogenous normalizing genes, and relative expression was calculated using the 2-ΔCt method. Bars represent 5% standard error.
DOI: 10.6084/m9.figshare.10802150.v1
title: Raw qPCR data

description: (A) Expression of the new TlicBgluc gene was evaluated by qPCR at different stages of insect life (egg, larval stage early –ELI, late larval stage - LLI, pupa, moth) to determine the stage at which the gene exhibits higher expression. According to the results, the gene was widely expressed throughout the insect's life cycle, but expression increased significantly at the late larval stage (LLI), when the insect required most glucose utilization. (B) In the larval stage, TlicBgluc expression was evaluated in the midgut and carcass. Gene transcripts are massively detected in the gut. TlicGAPDH and TlicRPS18 were chosen as endogenous normalizing genes, and relative expression was calculated using the 2-ΔCt method. Bars represent 5% standard error.
DOI: 10.6084/m9.figshare.10786607
title: service quality in higher education paper.sav

description: This data includes SPSS spreadsheet coding data generated to assess the relationship among service quality, student satisfaction and loyalty in the higher educational institutions.<br>
DOI: 10.5522/04/10783589
title: Ab initio calculations and high P-T experiments on iron, iron alloys and other materials: Carbon partitioning between solid and liquid iron

description: This folder includes the alchemical thermodynamic integration free energy calculations for solid and liquid Fe-C alloys at 360 GPa and 6500 K. The chemical potential of C can be integrating the free energy difference. Five equally spaced points were used for each integration. The ab initio molecular dynamics calculations were performed by using the Vienna Ab initio Simulation Package.
DOI: 10.5522/04/10782161
title: Ab initio calculations and high P-T experiments on iron, iron alloys and other materials: hcp-Fe-Si-C SQS structure

description: The folder contains the structures used for the cluster expansion for the hcp-Fe-Si-C alloy by using ATAT code.It also contains the Monte Carlo calculations for the production of special quasirandom structures of the hcp-Fe-Si-C alloy.
DOI: 10.6084/m9.figshare.10781795
title: Supplementary dataset

description: Supplementary dataset for "Emergence of a novel Salmonella enterica serotype Reading clone is linked to its expansion in commercial turkey production, resulting in unanticipated human illness in North America"
DOI: 10.5522/04/10783589.v1
title: Ab initio calculations and high P-T experiments on iron, iron alloys and other materials: Carbon partitioning between solid and liquid iron

description: This folder includes the alchemical thermodynamic integration free energy calculations for solid and liquid Fe-C alloys at 360 GPa and 6500 K. The chemical potential of C can be integrating the free energy difference. Five equally spaced points were used for each integration. The ab initio molecular dynamics calculations were performed by using the Vienna Ab initio Simulation Package.
DOI: 10.5522/04/10782161.v1
title: Ab initio calculations and high P-T experiments on iron, iron alloys and other materials: hcp-Fe-Si-C SQS structure

description: The folder contains the structures used for the cluster expansion for the hcp-Fe-Si-C alloy by using ATAT code.It also contains the Monte Carlo calculations for the production of special quasirandom structures of the hcp-Fe-Si-C alloy.
DOI: 10.6084/m9.figshare.10781795.v1
title: Supplementary dataset

description: Supplementary dataset for "Emergence of a novel Salmonella enterica serotype Reading clone is linked to its expansion in commercial turkey production, resulting in unanticipated human illness in North America"
DOI: 10.6084/m9.figshare.10780820.v1
title: Example Data

description: Data of the example datasets of the tutorial. The archive contains one two directories: one for each of the protocol shown in the tutorial.Protocol 1 contains the marker genes and the Multiple Sequence Alignments (MSA), as well as trees obtained from two reconstruction methods (IqTree and RaXML).Protocol 2 contains the OMA Standalone directory, the locally added genomes, the selected Orthologous Groups, and their MSA, as well as the trees from two reconstruction methods.
DOI: 10.6084/m9.figshare.10773641
title: Ca3-xSrxTi2O7_simdata.zip

description: Output files from simulations, mode amplitudes found using amplimodes and scripts to generate paper figures.
DOI: 10.6084/m9.figshare.10780820.v2
title: Phylogenetic Tree Tutorial Example Data

description: Data of the example datasets of the tutorial. The archive contains one two directories: one for each of the protocol shown in the tutorial.Protocol 1 contains the marker genes and the Multiple Sequence Alignments (MSA), as well as trees obtained from two reconstruction methods (IqTree and RaXML).Protocol 2 contains the OMA Standalone directory, the locally added genomes, the selected Orthologous Groups, and their MSA, as well as the trees from two reconstruction methods.
DOI: 10.6084/m9.figshare.10773641.v1
title: Ca3-xSrxTi2O7_simdata.zip

description: Output files from simulations, mode amplitudes found using amplimodes and scripts to generate paper figures.