cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14513529
title: I-Seed_DS8 – Laboratory (internal/controlled conditions) test data:  initial test of sensors

description: This file describes the datasets which have been prepared for WP10 on calibration and validation tests in a laboratory environment, under controlled conditions of I-Seed sensors (both Samara and Chimera final design) using the sensing material provided by INM. It contains the datafiles for the calibration curves for each environmental parameter to associate the optical measurement, obtained from the fluorescence emission from laser irradiation, with a corresponding value of Hg and CO2 concentration, and T, to assess response linearity and also accuracy compared to the conventional/standard techniques.

The following zip file have been prepared: RH & Air-Tem_DATA_2023: calibration measurements for T and RH sensor under controlled conditions;

RH & Air-Tem_DATA_2024: calibration measurements for T and RH sensor under controlled conditions;

Hg-sensors_Tests_Decreasing Rate: calibration measurements for Hg sensors using CVAFS technique under controlled conditions;

Hg_Sensors_Test_s3-s4-s5-s6-s7_Perm Source_5min: calibration measurements for Hg sensors using CVAFS technique under controlled conditions;

Hg_Sensors_Tests: figures_ppt contains a summarized ppt file providing an overview of the Hg experiment using CVAFS technique under controlled conditions; 

CO2 Elab_Tests: calibration measurements for CO2 sensors under controlled conditions;

Data_20240122.Elab_txt: file providing an overview of the experiment raw data:

Every .xls file contains a folder structure summarizing figures, overview of the experiment under controlled conditions for calibration and validation tests considering decreasing rate, permeation source, kinetics decay, regression line, measurements with different injections etc..
DOI: 10.5281/zenodo.14513530
title: I-Seed_DS8 – Laboratory (internal/controlled conditions) test data:  initial test of sensors

description: This file describes the datasets which have been prepared for WP10 on calibration and validation tests in a laboratory environment, under controlled conditions of I-Seed sensors (both Samara and Chimera final design) using the sensing material provided by INM. It contains the datafiles for the calibration curves for each environmental parameter to associate the optical measurement, obtained from the fluorescence emission from laser irradiation, with a corresponding value of Hg and CO2 concentration, and T, to assess response linearity and also accuracy compared to the conventional/standard techniques.

The following zip file have been prepared: RH & Air-Tem_DATA_2023: calibration measurements for T and RH sensor under controlled conditions;

RH & Air-Tem_DATA_2024: calibration measurements for T and RH sensor under controlled conditions;

Hg-sensors_Tests_Decreasing Rate: calibration measurements for Hg sensors using CVAFS technique under controlled conditions;

Hg_Sensors_Test_s3-s4-s5-s6-s7_Perm Source_5min: calibration measurements for Hg sensors using CVAFS technique under controlled conditions;

Hg_Sensors_Tests: figures_ppt contains a summarized ppt file providing an overview of the Hg experiment using CVAFS technique under controlled conditions; 

CO2 Elab_Tests: calibration measurements for CO2 sensors under controlled conditions;

Data_20240122.Elab_txt: file providing an overview of the experiment raw data:

Every .xls file contains a folder structure summarizing figures, overview of the experiment under controlled conditions for calibration and validation tests considering decreasing rate, permeation source, kinetics decay, regression line, measurements with different injections etc..
DOI: 10.6084/m9.figshare.c.3875785_d3.v1
title: Additional file 3: Table S2. of Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

description: The diet-responsive probes identified by RP (PFPÂ
DOI: 10.6084/m9.figshare.c.3875785_d3
title: Additional file 3: Table S2. of Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

description: The diet-responsive probes identified by RP (PFPÂ
DOI: 10.6084/m9.figshare.c.3875785_d4.v1
title: Additional file 4: Table S3. of Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

description: Complete list of significantly pIC- responsive probes identified by SAM (FDR
DOI: 10.6084/m9.figshare.c.3875785_d4
title: Additional file 4: Table S3. of Transcriptome profiling of antiviral immune and dietary fatty acid dependent responses of Atlantic salmon macrophage-like cells

description: Complete list of significantly pIC- responsive probes identified by SAM (FDR
DOI: 10.15468/dl.uwxmbv
title: Occurrence Download

description: A dataset listing the 45 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fucus vesiculosus L."
 ]
}

 The dataset's 45 records were derived from 302 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039342-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qk42sj
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Ambystoma cingulatum Cope, 1868)"
 ]
}

 The dataset includes 99 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039358-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14515186
title: Ciência, Tecnologia, Sociedade e Ambiente (respostas)
DOI: 10.5281/zenodo.14515187
title: Ciência, Tecnologia, Sociedade e Ambiente (respostas)
DOI: 10.15468/dl.ht7b7r
title: Occurrence Download

description: A dataset listing the 4 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is Species composition and distribution of anopheles gambiae complex circulating in Kinshasa"
 ]
}

 The dataset's 4 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039345-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3877027_d2
title: Additional file 2: Table S1. of De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

description: Shows differentially expressed coral genes along with results from pairwise tissue type comparisons, gene annotations, annotation sources, and gene expression statistics. (XLS 172 kb)
DOI: 10.6084/m9.figshare.c.3877027_d2.v1
title: Additional file 2: Table S1. of De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly

description: Shows differentially expressed coral genes along with results from pairwise tissue type comparisons, gene annotations, annotation sources, and gene expression statistics. (XLS 172 kb)
DOI: 10.6084/m9.figshare.c.3877030_d2
title: Additional file 2: of How driving endonuclease genes can be used to combat pests and disease vectors

description: A compiled computer programme written in Mathematica, that allows further exploration of the CATCHA mechanism (see Additional file 1: Note 16). (CDF 44 kb)
DOI: 10.6084/m9.figshare.c.3877030_d2.v1
title: Additional file 2: of How driving endonuclease genes can be used to combat pests and disease vectors

description: A compiled computer programme written in Mathematica, that allows further exploration of the CATCHA mechanism (see Additional file 1: Note 16). (CDF 44 kb)
DOI: 10.6084/m9.figshare.c.3877030_d3.v1
title: Additional file 3: of How driving endonuclease genes can be used to combat pests and disease vectors

description: A compiled computer programme that allow classic homing gene drive and driving Y chromosomes to be explored separately and together (see Additional file 1: Note 19). (CDF 144 kb)
DOI: 10.6084/m9.figshare.c.3877039_d3.v1
title: Additional file 3: Table ST2. of Determining the optimal number of independent components for reproducible transcriptomic data analysis

description: Genes associated with ICA components of the METABRIC dataset, in the case when a component is driven by a small group of genes (frequently, one gene). Gene names marked in bold also drive independent components in several other breast cancer datasets and the corresponding components are reciprocally reproducible in terms of the correlation of the whole ICA-based metagenes. (XLSX 10Â kb)
DOI: 10.5281/zenodo.14500521
title: Baargin annotation and analysis of draft genomes of six Methicillin-Resistant Staphylococcus aureus in a Philippine tertiary hospital

description: This dataset contains the annotation (using Prokka v.1.14.5 [1]) and antimicrobial resistance genes analysis files (using the AMRFinderPlus v.2024-05-02.2 [2] database) generated from the baargin pipeline [3] genome analysis of six Methicillin-Resistant Staphylococcus aureus (TMCC-SA1, -SA3, -SA5, -SA6, -SA8, and -SA18) isolated from a tertiary hospital in the Philippines. The baargin pipeline was used as an extended analysis of the assembled genomes, complementing the preliminary Prokaryotic Genome Annotation Pipeline (PGAP). The genome assemblies and preliminary PGAP annotation are available at NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/) under the BioProject number PRJNA1157534.

This dataset is part of the study: Carascal MB, Gonzales JE, Tañedo MMJ, Papa DM, Destura RV, and Henson KE. Draft genomes of six Methicillin-Resistant Staphylococcus aureus in a Philippine tertiary hospital with insights on antimicrobial and phage resistance mechanisms [submitted for publication at the Microbiology Resource Announcements].

 

References:

[1] Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinforma Oxf Engl 30:2068–2069.

[2] Feldgarden M, Brover V, Gonzalez-Escalona N, Frye J, Haendiges J, Haft D, et al. 2021. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Nat Sci Rep 11:12728.

[3] Hayer J, Dainat J, Marcy E, Bañuls AL. Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance. Journal of Open Source Software 2023;8(90): 5397.
DOI: 10.5281/zenodo.14500522
title: Baargin annotation and analysis of draft genomes of six Methicillin-Resistant Staphylococcus aureus in a Philippine tertiary hospital

description: This dataset contains the annotation (using Prokka v.1.14.5 [1]) and antimicrobial resistance genes analysis files (using the AMRFinderPlus v.2024-05-02.2 [2] database) generated from the baargin pipeline [3] genome analysis of six Methicillin-Resistant Staphylococcus aureus (TMCC-SA1, -SA3, -SA5, -SA6, -SA8, and -SA18) isolated from a tertiary hospital in the Philippines. The baargin pipeline was used as an extended analysis of the assembled genomes, complementing the preliminary Prokaryotic Genome Annotation Pipeline (PGAP). The genome assemblies and preliminary PGAP annotation are available at NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/) under the BioProject number PRJNA1157534.

This dataset is part of the study: Carascal MB, Gonzales JE, Tañedo MMJ, Papa DM, Destura RV, and Henson KE. Draft genomes of six Methicillin-Resistant Staphylococcus aureus in a Philippine tertiary hospital with insights on antimicrobial and phage resistance mechanisms [submitted for publication at the Microbiology Resource Announcements].

 

References:

[1] Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinforma Oxf Engl 30:2068–2069.

[2] Feldgarden M, Brover V, Gonzalez-Escalona N, Frye J, Haendiges J, Haft D, et al. 2021. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Nat Sci Rep 11:12728.

[3] Hayer J, Dainat J, Marcy E, Bañuls AL. Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance. Journal of Open Source Software 2023;8(90): 5397.
DOI: 10.6084/m9.figshare.c.3877030_d3
title: Additional file 3: of How driving endonuclease genes can be used to combat pests and disease vectors

description: A compiled computer programme that allow classic homing gene drive and driving Y chromosomes to be explored separately and together (see Additional file 1: Note 19). (CDF 144 kb)
DOI: 10.6084/m9.figshare.c.3877066_d2
title: Additional file 11: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Average of base composition (AT- and GC-content) of mature, star and precursor regions of the selected conserved and non-conserved miRNA genes of Oryza. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3877072_d1.v1
title: Additional file 1: Table S1. of 
                     BRCA2 carriers with male breast cancer show elevated tumour methylation

description: REMARK patient flow through study (XLSX 34 kb)
DOI: 10.15468/dl.8rjh5h
title: Occurrence Download

description: A dataset containing 99 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "TaxonKey is one of (Ambystoma cingulatum Cope, 1868)"
 ]
}

 The dataset includes 99 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039360-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3877066_d3.v1
title: Additional file 12: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: The values of Tajima’s D and Fu and Li’s F as well as nucleotide diversity for each of the 80 miRNA loci (pre-miRNAs) from the 10 Oryza species. The parameters were computed using software DnaSP v5.10. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3877072_d1
title: Additional file 1: Table S1. of 
                     BRCA2 carriers with male breast cancer show elevated tumour methylation

description: REMARK patient flow through study (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3877066_d3
title: Additional file 12: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: The values of Tajima’s D and Fu and Li’s F as well as nucleotide diversity for each of the 80 miRNA loci (pre-miRNAs) from the 10 Oryza species. The parameters were computed using software DnaSP v5.10. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3877072_d2.v1
title: Additional file 2: Table S2. of 
                     BRCA2 carriers with male breast cancer show elevated tumour methylation

description: Methylation specific high resolution melting condition and primers (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3877072_d2
title: Additional file 2: Table S2. of 
                     BRCA2 carriers with male breast cancer show elevated tumour methylation

description: Methylation specific high resolution melting condition and primers (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3877081_d1
title: Additional file 1: of Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes

description: Normalized dataset. (XLSX 3589Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d5.v1
title: Additional file 14: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: The average sequence diversity (Ď ) at the 11 miRNA loci (with the significantly negative values for D and F) in cultivated rice and wild species of Oryza. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d5
title: Additional file 14: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: The average sequence diversity (Ď ) at the 11 miRNA loci (with the significantly negative values for D and F) in cultivated rice and wild species of Oryza. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d8
title: Additional file 17: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Percent identity matrix showing the identity among the nine different clusters of osa-miR1861 family in rice. (TXT 1003 bytes)
DOI: 10.6084/m9.figshare.c.3877084_d3
title: Additional file 3: Table S2. of More than 2500Â years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

description: MG-RAST metagenomes analyzed and compared to Keri Lake samples and their features. The metagenomes are grouped in stabilized and perturbed based on the time they are exposed to oil. (XLS 35Â kb)
DOI: 10.6084/m9.figshare.c.3877081_d3.v1
title: Additional file 3: of Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes

description: Overlaps of significantly changed mutant probe sets and putative canonical/non-canonical transcriptional target classification. (XLSX 138Â kb)
DOI: 10.6084/m9.figshare.c.3877081_d3
title: Additional file 3: of Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes

description: Overlaps of significantly changed mutant probe sets and putative canonical/non-canonical transcriptional target classification. (XLSX 138Â kb)
DOI: 10.6084/m9.figshare.c.3877090_d3.v1
title: Additional file 3: Table S12. of Clinical characteristics of adrenal crisis in adult population with and without predisposing chronic adrenal insufficiency: a retrospective cohort study

description: Review of previous studies. (XLS 41 kb)
DOI: 10.6084/m9.figshare.c.3877084_d5.v1
title: Additional file 5: Table S3. of More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

description: Summary of samples obtained from the NE and HΕ sites to asphalt oil. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3877084_d5
title: Additional file 5: Table S3. of More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

description: Summary of samples obtained from the NE and HΕ sites to asphalt oil. (XLS 36 kb)
DOI: 10.6084/m9.figshare.c.3877090_d3
title: Additional file 3: Table S12. of Clinical characteristics of adrenal crisis in adult population with and without predisposing chronic adrenal insufficiency: a retrospective cohort study

description: Review of previous studies. (XLS 41 kb)
DOI: 10.6084/m9.figshare.c.3877099_d2.v1
title: Additional file 2 of Lessons from a decade of individual-based models for infectious disease transmission: a systematic review (2006-2015)

description: Reference list. List of the included studies using an individual-based model to study infectious disease transmission. References are sorted by topic and disease and listed together with their terminology, modeling purpose, (non)inclusion of an economic analysis, intervention strategy and methodology classification. (CSV 183 kb)
DOI: 10.6084/m9.figshare.c.3877066_d11.v1
title: Additional file 1: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Details of different orthologous miRNAs of O. sativa (japonica) from the ten diploid Oryza species. oba- (O. barthi), obr- (O. brachyantha), ogl- (O. glaberrima), oglu- (O. glumaepatula), olo- (O.longistaminata), ome- (O. meridionalis), oni- (O. nivara), opu- (O. punctata), oru- (O. rufipogon), osi- (O. sativa subsp. indica). (XLSX 867Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d11
title: Additional file 1: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Details of different orthologous miRNAs of O. sativa (japonica) from the ten diploid Oryza species. oba- (O. barthi), obr- (O. brachyantha), ogl- (O. glaberrima), oglu- (O. glumaepatula), olo- (O.longistaminata), ome- (O. meridionalis), oni- (O. nivara), opu- (O. punctata), oru- (O. rufipogon), osi- (O. sativa subsp. indica). (XLSX 867Â kb)
DOI: 10.6084/m9.figshare.c.3877081_d5
title: Additional file 5: of Canonical and non-canonical JAK/STAT transcriptional targets may be involved in distinct and overlapping cellular processes

description: Heterochromatin marker modENCODE enrichment and transcriptional target overlaps. (XLSX 56Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d14.v1
title: Additional file 4: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Average no. of nucleotide substitutions per site in different regions of miRNA genes, transition/transversion bias as well as rates of nucleotide substitutions in conserved and non-conserved miRNA genes along with all the protein coding genes of Oryza. JC-values (Jukes Cantor-values). (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d14
title: Additional file 4: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Average no. of nucleotide substitutions per site in different regions of miRNA genes, transition/transversion bias as well as rates of nucleotide substitutions in conserved and non-conserved miRNA genes along with all the protein coding genes of Oryza. JC-values (Jukes Cantor-values). (XLSX 12Â kb)
DOI: 10.15468/dl.fv4jc6
title: Occurrence Download

description: A dataset containing 11898 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zostera noltii Hornem."
 ]
}

 The dataset includes 11898 records from 250 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0039361-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.c.3877066_d16.v1
title: Additional file 6: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Ka/Ks ratios of all orthologous protein-coding genes of 10 Oryza species. Ratios were calculated using GrameneMart. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3877066_d16
title: Additional file 6: of Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species

description: Ka/Ks ratios of all orthologous protein-coding genes of 10 Oryza species. Ratios were calculated using GrameneMart. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3877129_d4
title: Additional file 4: of Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons

description: GO biological process annotation in S. mimosarum. (XLSX 93Â kb)
DOI: 10.6084/m9.figshare.c.3877129_d5
title: Additional file 5: of Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons

description: List of conserved genes associated with RNA-splicing PPI across D. melanogaster, H. sapiens, A. thaliana, and S. cerevisiae comparisons. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3877129_d5.v1
title: Additional file 5: of Predicted networks of protein-protein interactions in Stegodyphus mimosarum by cross-species comparisons

description: List of conserved genes associated with RNA-splicing PPI across D. melanogaster, H. sapiens, A. thaliana, and S. cerevisiae comparisons. (XLSX 13Â kb)