cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6831416
title: Additional file 3: of A model for predicting utilization of mHealth interventions in low-resource settings: case of maternal and newborn care in Kenya

description: Pretest dataset obtained from randomly selected antenatal and post-natal women. The dataset was used as the baseline for predicting post-deployment utilization of mamacare services. (CSV 5Â kb)
DOI: 10.6084/m9.figshare.6831416.v1
title: Additional file 3: of A model for predicting utilization of mHealth interventions in low-resource settings: case of maternal and newborn care in Kenya

description: Pretest dataset obtained from randomly selected antenatal and post-natal women. The dataset was used as the baseline for predicting post-deployment utilization of mamacare services. (CSV 5Â kb)
DOI: 10.6084/m9.figshare.6831410
title: Additional file 2: of Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints

description: The RSCU values of each sequence and the first 2 PCA factors. This file contains all the calculated RSCU values of each sequence and the first 2 PCA factors. The stop codons were not included and thusly this file has 62 columns. The beginning of each column shows the specific meanings of the different value types. (XLSX 6743 kb)
DOI: 10.6084/m9.figshare.6831410.v1
title: Additional file 2: of Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints

description: The RSCU values of each sequence and the first 2 PCA factors. This file contains all the calculated RSCU values of each sequence and the first 2 PCA factors. The stop codons were not included and thusly this file has 62 columns. The beginning of each column shows the specific meanings of the different value types. (XLSX 6743 kb)
DOI: 10.6084/m9.figshare.6831395
title: Additional file 1: of Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis

description: Table S1. Summary of genome sequencing quality and reads mapping quality. Table S2. Comparison of quality assessment and assembly statistics of two methods. Table S3. Comparison of GO classifications of annotated genes for P. multiseries, P. tricornutum and Mn4. Table S4. Genomes for the other organisms in this study. Table S5. Classification of duplicate gene origins in the thraustochytridsâ genomes. Table S6. Statistics for IPR domains enriched in thraustochytrids compared to outgroups. Table S7. Statistics for IPR domains depleted in thraustochytrids compared to outgroups. Table S8. Distribution of CAZy Families in genomes of thraustochytrids. Table S9. Distribution of CAZy Families in secretomes of thraustochytrids. Table S10. Statistics for the up-regulated /down-regulated genes identified in two different groups. Table S11. The transcriptional expression levels of secreted CAZyme genes in Mn4. Table S12. Expression of genes related to DHA biosynthesis of the FAS pathway in Mn4. Table S13. Summary of polyketide synthase (PKS) gene clusters in thraustochytrids. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.6831395.v1
title: Additional file 1: of Comparative analysis reveals unexpected genome features of newly isolated Thraustochytrids strains: on ecological function and PUFAs biosynthesis

description: Table S1. Summary of genome sequencing quality and reads mapping quality. Table S2. Comparison of quality assessment and assembly statistics of two methods. Table S3. Comparison of GO classifications of annotated genes for P. multiseries, P. tricornutum and Mn4. Table S4. Genomes for the other organisms in this study. Table S5. Classification of duplicate gene origins in the thraustochytridsâ genomes. Table S6. Statistics for IPR domains enriched in thraustochytrids compared to outgroups. Table S7. Statistics for IPR domains depleted in thraustochytrids compared to outgroups. Table S8. Distribution of CAZy Families in genomes of thraustochytrids. Table S9. Distribution of CAZy Families in secretomes of thraustochytrids. Table S10. Statistics for the up-regulated /down-regulated genes identified in two different groups. Table S11. The transcriptional expression levels of secreted CAZyme genes in Mn4. Table S12. Expression of genes related to DHA biosynthesis of the FAS pathway in Mn4. Table S13. Summary of polyketide synthase (PKS) gene clusters in thraustochytrids. (XLSX 101 kb)
DOI: 10.6084/m9.figshare.6831383
title: Additional file 1: of Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints

description: The values of ENC, expected ENC, GC content, protein length, GRAVY, and AROMO. This file contains the calculated values of ENC, expected ENC, GC content, protein length, GRAVY, and AROMO. Different columns represent different value types, and their specific meanings were shown at the beginning of each column. (XLSX 1818 kb)
DOI: 10.6084/m9.figshare.6831383.v1
title: Additional file 1: of Analysis of codon usage patterns in Hirudinaria manillensis reveals a preference for GC-ending codons caused by dominant selection constraints

description: The values of ENC, expected ENC, GC content, protein length, GRAVY, and AROMO. This file contains the calculated values of ENC, expected ENC, GC content, protein length, GRAVY, and AROMO. Different columns represent different value types, and their specific meanings were shown at the beginning of each column. (XLSX 1818 kb)
DOI: 10.6084/m9.figshare.12888500
title: WGS of highland mexicana and maize landrace populations in Mexico - metadata and SRA accessions

description: NCBI SRA BioProject PRJNA657016 contains publicly available metadata and whole-genome-sequence fastq files for a total of 348 Zea mays individuals. This data was generated to analyze admixture between maize grown in the mountains of Mexico and an endemic wild relative, mexicana. This study seeks to identify adaptively introgressed loci from mexicana into maize that may be associated with key genetic adaptations for growing at high elevations. More broadly, this genomic dataset is being used to better understand the evolutionary consequences of secondary contact and gene flow in this domesticated and wild subspecies pair. Sequenced individuals were sampled in the highlands of Mexico from 14 sympatric maize-mexicana sympatric population pairs and 3 allopatric mexicana populations. Link to NCBI SRA: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA657016/
DOI: 10.6084/m9.figshare.6831350
title: Additional file 1: of Quality of care for children with acute malnutrition at health center level in Uganda: a cross sectional study in West Nile region during the refugee crisis

description: Quantitative dataset. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.6831350.v1
title: Additional file 1: of Quality of care for children with acute malnutrition at health center level in Uganda: a cross sectional study in West Nile region during the refugee crisis

description: Quantitative dataset. (XLSX 57 kb)
DOI: 10.6084/m9.figshare.12888500.v1
title: WGS of highland mexicana and maize landrace populations in Mexico - metadata and SRA accessions

description: NCBI SRA BioProject PRJNA657016 contains publicly available metadata and whole-genome-sequence fastq files for a total of 348 Zea mays individuals. This data was generated to analyze admixture between maize grown in the mountains of Mexico and an endemic wild relative, mexicana. This study seeks to identify adaptively introgressed loci from mexicana into maize that may be associated with key genetic adaptations for growing at high elevations. More broadly, this genomic dataset is being used to better understand the evolutionary consequences of secondary contact and gene flow in this domesticated and wild subspecies pair. Sequenced individuals were sampled in the highlands of Mexico from 14 sympatric maize-mexicana sympatric population pairs and 3 allopatric mexicana populations. Link to NCBI SRA: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA657016/
DOI: 10.6084/m9.figshare.6831347
title: MOESM3 of Self-assembling functional programmable protein array for studying protein–protein interactions in malaria parasites

description: Additional file 3: Table S1. List of primers used, amplicon size, expressed products’ molecular weight and destination vectors for the genes analysed.
DOI: 10.6084/m9.figshare.6831347.v1
title: MOESM3 of Self-assembling functional programmable protein array for studying protein–protein interactions in malaria parasites

description: Additional file 3: Table S1. List of primers used, amplicon size, expressed products’ molecular weight and destination vectors for the genes analysed.
DOI: 10.6084/m9.figshare.6831341
title: Additional file 1 of Gastroesophageal reflux symptoms among Italian university students: epidemiology and dietary correlates using automatically recorded transactions

description: Supplementary tables. (TEX 11 kb)
DOI: 10.6084/m9.figshare.6831341.v1
title: Additional file 1 of Gastroesophageal reflux symptoms among Italian university students: epidemiology and dietary correlates using automatically recorded transactions

description: Supplementary tables. (TEX 11 kb)
DOI: 10.6084/m9.figshare.6831305
title: Additional file 3: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

description: Figure S1. Differential methylated sites. Representation of the amount of methylated sites per gene and per patient subset. The amount of hypermethylated sites per gene can be found on the y-axis, both for hypermethylated sites in non-malignant lung tissue (blue) and hypermethylated sites in tumor tissue (red). Associations with histone markers and CpG islands are color coded per methylation site. P-values can be equal across different subsets and genes for non-significant results because of the statistical method used. (XLSM 509 kb)
DOI: 10.6084/m9.figshare.6831305.v1
title: Additional file 3: of RNA-sequencing in non-small cell lung cancer shows gene downregulation of therapeutic targets in tumor tissue compared to non-malignant lung tissue

description: Figure S1. Differential methylated sites. Representation of the amount of methylated sites per gene and per patient subset. The amount of hypermethylated sites per gene can be found on the y-axis, both for hypermethylated sites in non-malignant lung tissue (blue) and hypermethylated sites in tumor tissue (red). Associations with histone markers and CpG islands are color coded per methylation site. P-values can be equal across different subsets and genes for non-significant results because of the statistical method used. (XLSM 509 kb)
DOI: 10.6084/m9.figshare.6831257
title: MOESM5 of PBMC fixation and processing for Chromium single-cell RNA sequencing

description: Additional file 5: Table S3. Sequencing metrics summary of 10 scRNA-Seq datasets.
DOI: 10.6084/m9.figshare.6831257.v1
title: MOESM5 of PBMC fixation and processing for Chromium single-cell RNA sequencing

description: Additional file 5: Table S3. Sequencing metrics summary of 10 scRNA-Seq datasets.
DOI: 10.6084/m9.figshare.6831200
title: MOESM2 of PBMC fixation and processing for Chromium single-cell RNA sequencing

description: Additional file 2: Table S2. Marker genes used for identifying PBMC subpopulations.
DOI: 10.6084/m9.figshare.6831200.v1
title: MOESM2 of PBMC fixation and processing for Chromium single-cell RNA sequencing

description: Additional file 2: Table S2. Marker genes used for identifying PBMC subpopulations.
DOI: 10.6084/m9.figshare.6831173
title: MOESM1 of PBMC fixation and processing for Chromium single-cell RNA sequencing

description: Additional file 1: Table S1. Potential impacts on single cell transcriptome analysis after cell fixation.
DOI: 10.6084/m9.figshare.6831173.v1
title: MOESM1 of PBMC fixation and processing for Chromium single-cell RNA sequencing

description: Additional file 1: Table S1. Potential impacts on single cell transcriptome analysis after cell fixation.
DOI: 10.6084/m9.figshare.6830945.v1
title: GraphData_Figure 3.docx

description: Data underlying Figure 3 of O'Neill et al 2018 Gates Open Research
DOI: 10.6084/m9.figshare.6830282
title: STRetch summary statistics from 97 PCR-free whole genomes

description: Robust median and variance estimates for all STR loci (based on the hg19 TRF annotation) for which any evidence of expansion has been observed in 97 PCR-free whole genomes. This file is generated by using the STRetch estimateSTR.py script with the --emit flag (see https://github.com/Oshlack/STRetch).<br>
DOI: 10.6084/m9.figshare.6829235
title: Raw data for Turf Algal MS

description: These files support a published manuscript describing the impact of ocean acidification on the growth and diversity of turf algal communities associated with coral reefs.
DOI: 10.6084/m9.figshare.6829292
title: Smith Federmeier 2018 LCN Processed EEG Data

description: EEG data accompanying Smith & Federmeier (2018, LCN). All EEG results should be derivable from this file, which includes mean voltages from 300-500 and 500-900 ms for all word stimuli in the experiment. Please see README.rtf file for column descriptions and publication for further details about the experimental design, etc.
DOI: 10.6084/m9.figshare.6829235.v1
title: Raw data for Turf Algal MS

description: These files support a published manuscript describing the impact of ocean acidification on the growth and diversity of turf algal communities associated with coral reefs.
DOI: 10.6084/m9.figshare.6829292.v2
title: Smith Federmeier 2018 LCN Processed EEG Data

description: EEG data accompanying Smith & Federmeier (2018, LCN). All EEG results should be derivable from this file, which includes mean voltages from 300-500 and 500-900 ms for all word stimuli in the experiment. Please see README.rtf file for column descriptions and publication for further details about the experimental design, etc.
DOI: 10.6084/m9.figshare.6829292.v1
title: Smith Federmeier 2018 LCN Processed EEG Data

description: EEG data accompanying Smith & Federmeier (2018, LCN). All EEG results should be derivable from this file, which includes mean voltages from 300-500 and 500-900 ms for all word stimuli in the experiment. Please see README.rtf file for column descriptions and publication for further details about the experimental design, etc.
DOI: 10.6084/m9.figshare.6829064
title: Wireless-Philosophy-Consent-Part-1-Tom-Dougherty

description: Tom Dougherty considers the nature of consent.
DOI: 10.6084/m9.figshare.6828968
title: Effects of predators on sedimentary carbon storage in Heron Island Lagoon

description: Data provides sediment and algae characteristic for collections at Heron Island Lagoon.
DOI: 10.6084/m9.figshare.6828968.v1
title: Effects of predators on sedimentary carbon storage in Heron Island Lagoon

description: Data provides sediment and algae characteristic for collections at Heron Island Lagoon.
DOI: 10.6084/m9.figshare.6828848
title: Southeast Pine Savannas and Woodlands Range Map

description: Geographic ranges of pine savanna and woodland vegetation types in the southeastern U.S. Divisions are based on abundance of overstory trees and ground-layer grasses. <br>Data for Figure in:Peet, R.K., Platt, W.J., Costanza, J.K. 2018. The ecology and management of fire-maintained savanna ecosystems of the Southeastern U.S. Coastal Plain. Chapter in: Ecology and Recovery of Eastern Old-Growth Forests. Editors: Keeton, W., Barton, A., Island Press, Washington, D.C., USA, pp. 39-62
DOI: 10.6084/m9.figshare.6828776
title: A simple, rapid and novel method based on salting-out assisted liquid–liquid extraction for ochratoxin A determination in beer samples prior to ultra-high-performance liquid chromatography coupled to tandem mass spectrometry

description: A novel, simple, easy and cheap sample treatment strategy based on salting-out assisted liquid-liquid extraction for ochratoxin A (OTA) ultra-trace analysis in beer samples using ultra-high-performance liquid chromatography-tandem mass spectrometry determination was developed. The factors involved in the efficiency of pre-treatment were studied employing factorial design in the screening phase and the optimal conditions of the significant variables on the analytical response were evaluated using a central composite face-centred design. Consequently, the amount of salt ((NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>), together with the volumes of sample, hydrophilic (acetone) and nonpolar (toluene) solvents, and times of vortexing and centrifugation were optimised. Under optimised conditions, the limits of detection and quantification were 0.02 µg l<sup>−1</sup> and 0.08 µg l<sup>−1</sup> respectively. OTA extraction recovery by SALLE was approximately 90% (0.2 µg l<sup>−1</sup>). Furthermore, the methodology was in agreement with EU Directive requirements and was successfully applied for analysis of beer samples.
DOI: 10.6084/m9.figshare.6828776.v1
title: A simple, rapid and novel method based on salting-out assisted liquid–liquid extraction for ochratoxin A determination in beer samples prior to ultra-high-performance liquid chromatography coupled to tandem mass spectrometry

description: A novel, simple, easy and cheap sample treatment strategy based on salting-out assisted liquid-liquid extraction for ochratoxin A (OTA) ultra-trace analysis in beer samples using ultra-high-performance liquid chromatography-tandem mass spectrometry determination was developed. The factors involved in the efficiency of pre-treatment were studied employing factorial design in the screening phase and the optimal conditions of the significant variables on the analytical response were evaluated using a central composite face-centred design. Consequently, the amount of salt ((NH<sub>4</sub>)<sub>2</sub>SO<sub>4</sub>), together with the volumes of sample, hydrophilic (acetone) and nonpolar (toluene) solvents, and times of vortexing and centrifugation were optimised. Under optimised conditions, the limits of detection and quantification were 0.02 µg l<sup>−1</sup> and 0.08 µg l<sup>−1</sup> respectively. OTA extraction recovery by SALLE was approximately 90% (0.2 µg l<sup>−1</sup>). Furthermore, the methodology was in agreement with EU Directive requirements and was successfully applied for analysis of beer samples.
DOI: 10.6084/m9.figshare.6828848.v1
title: SE_pine_savannas_&_woodlands.zip

description: Geographic ranges of pine savanna and woodland types in the southeastern U.S. Divisions are based on abundance of overstory trees and ground-layer grasses. <br>Data for Figure 1 in:Peet, R.K., Platt, W.J., Costanza, J.K. 2018. The ecology and management of fire-maintained savanna ecosystems of the Southeastern U.S. Coastal Plain. Chapter in: Ecology and Recovery of Eastern Old-Growth Forests. Editors: Keeton, W., Barton, A., Island Press, Washington, D.C., USA (In press).
DOI: 10.6084/m9.figshare.6828725
title: Dataset.eng - Sun exposure

description: This dataset is product of a cross-sectional study in the Pimentel beach, Peru. Pimentel is one of the main beaches in the northern Peru and belongs to Lambayeque, which is considered a semi-warm and tropical-dry region, with temperatures that exceed 30°C during summer.<br>In 2018, we surveyed all the beachgoers from 8 a.m. to 4 p.m. and from March 5 to March 19 (Peruvian summer). No sample was calculated. We surveyed all Spanish-speaking adults aged 18 to 59 who were in the study place within the specified time range.
DOI: 10.6084/m9.figshare.6828722
title: Untitled Item

description: This dataset is product of a cross-sectional study in the Pimentel beach, Peru. Pimentel is one of the main beaches in the northern Peru and belongs to Lambayeque, which is considered a semi-warm and tropical-dry region, with temperatures that exceed 30°C during summer.<br>In 2018, we surveyed all the beachgoers from 8 a.m. to 4 p.m. and from March 5 to March 19 (Peruvian summer). No sample was calculated. We surveyed all Spanish-speaking adults aged 18 to 59 who were in the study place within the specified time range. <br>
DOI: 10.6084/m9.figshare.6828764.v1
title: R Script for data analysis used in the manuscript

description: R script to be used with the raw data in the same collection. Reproducible code for statistical analysis described in the paper (LME analysis and Wilcoxon tests)<br>
DOI: 10.6084/m9.figshare.6828722.v1
title: Untitled Item

description: This dataset is product of a cross-sectional study in the Pimentel beach, Peru. Pimentel is one of the main beaches in the northern Peru and belongs to Lambayeque, which is considered a semi-warm and tropical-dry region, with temperatures that exceed 30°C during summer.<br>In 2018, we surveyed all the beachgoers from 8 a.m. to 4 p.m. and from March 5 to March 19 (Peruvian summer). No sample was calculated. We surveyed all Spanish-speaking adults aged 18 to 59 who were in the study place within the specified time range. <br>
DOI: 10.6084/m9.figshare.6828617
title: Ukrainian Sentiment Dictionary from Polarized Ukraine 2014: opinion and territorial split demonstrated with the bounded confidence XY model, parameterized by twitter data

description: The file contains 2822 Ukrainian sentiment dictionary words scored on the scale from -5 to 5.
DOI: 10.6084/m9.figshare.6828617.v1
title: Ukrainian Sentiment Dictionary from Polarized Ukraine 2014: opinion and territorial split demonstrated with the bounded confidence XY model, parameterized by twitter data

description: The file contains 2822 Ukrainian sentiment dictionary words scored on the scale from -5 to 5.
DOI: 10.6084/m9.figshare.6827201
title: De novo assemblies, annotations, and gene expression profiling of gill epithelium from 16 species of Fundulus killifish in response to salinity change.

description: P51<br>Ion and Acid-Base Regulation in Fish Symposium#<strong>ICBF2018</strong><br>13th International Congress on the Biology of FishCalgary, Alberta, July 15-19, 2018<br>Estuaries are characterized by periodic fluxes in salinity. Many species of North American killifish (Fundulus) are estuarine specialists and harbor euryhaline phenotypes. Three clades within Fundulus independently radiated into freshwater environments and have lost their abilities to tolerate high salinity. We use Fundulus as a comparative model system for studying the physiological and genetic mechanisms that diverge between euryhaline and freshwater species. We examined 16 estuarine and freshwater species with representation from each of three clades. Fish from all species were acclimated to either brackish or fresh water then exposed to an acute brackish water challenge. Gill transcriptome data were collected. To enable multi-species comparisons, reference transcriptome assemblies were generated de novo for each species then used to analyze transcriptional responses to salinity change by clade and physiology. We find differences in the gene expression between euryhaline and freshwater species, some of which are shared across clades, implicating molecular mechanisms that contribute to divergent osmoregulatory physiologies.<br><br>Fundulus Multispecies Osmotic Transcriptome Sequencing Project (FMOTSP)<br>https://doi.org/10.17605/OSF.IO/M4XEG<br>Analysis scripts:https://github.com/ljcohen/RNAseq_15killifish<br>Raw data:https://www.ncbi.nlm.nih.gov/bioproject/473009<br>