cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3679030_d3
title: Additional file 2: of Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence

description: Gene ontology tables of genes with fast or slow decaying genes in both proliferating and quiescent fibroblasts. (XLSX 69Â kb)
DOI: 10.6084/m9.figshare.c.3679039_d1
title: Additional file 3: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Generating pileup files. Scripts and pipeline for pileup file generation. (HTML 223 kb)
DOI: 10.6084/m9.figshare.c.3679030_d4
title: Additional file 5: of Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence

description: Microarray determined gene expression values for proliferating versus 7-day contact inhibited or 14-day contact inhibited fibroblasts. (XLSX 1119Â kb)
DOI: 10.6084/m9.figshare.c.3679045_d1.v1
title: Additional file 1: Figure S1. of A case report of intravenous posaconazole in hepatic and renal impairment patient with invasive Aspergillus terreus infection: safety and role of therapeutic drug monitoring

description: Course of antifungal therapy, interventions, serum GM and plasma posaconazole levels. (XLSX 369 kb)
DOI: 10.6084/m9.figshare.c.3679045_d1
title: Additional file 1: Figure S1. of A case report of intravenous posaconazole in hepatic and renal impairment patient with invasive Aspergillus terreus infection: safety and role of therapeutic drug monitoring

description: Course of antifungal therapy, interventions, serum GM and plasma posaconazole levels. (XLSX 369 kb)
DOI: 10.6084/m9.figshare.c.3679039_d2.v1
title: Additional file 9: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Running MuTect on our dataset with default settings. Computational details and results of running MuTect on the described dataset without the tuning of the LOD parameter. (HTML 675 kb)
DOI: 10.6084/m9.figshare.c.3679039_d2
title: Additional file 9: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Running MuTect on our dataset with default settings. Computational details and results of running MuTect on the described dataset without the tuning of the LOD parameter. (HTML 675 kb)
DOI: 10.6084/m9.figshare.c.3679039_d3.v1
title: Additional file 8: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Running VarScan 2 on our dataset. Computational details and results of running VarScan 2 on the described dataset. (HTML 408 kb)
DOI: 10.6084/m9.figshare.c.3679039_d3
title: Additional file 8: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Running VarScan 2 on our dataset. Computational details and results of running VarScan 2 on the described dataset. (HTML 408 kb)
DOI: 10.6084/m9.figshare.c.3679039_d4.v1
title: Additional file 10: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Comparison of IsoMut and MuTect. Comparison of false positives rates when running IsoMut versus running MuTect with a finely tuned LOD parameter. (HTML 373 kb)
DOI: 10.6084/m9.figshare.c.3679039_d4
title: Additional file 10: of Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut

description: Comparison of IsoMut and MuTect. Comparison of false positives rates when running IsoMut versus running MuTect with a finely tuned LOD parameter. (HTML 373 kb)
DOI: 10.6084/m9.figshare.c.3679057_d1.v1
title: Additional file 2: Table S3. of Skewing in Arabidopsis roots involves disparate environmental signaling pathways

description: Comparing Col-0 to WS at different growth angles. (XLS 103 kb)
DOI: 10.6084/m9.figshare.c.3679057_d1
title: Additional file 2: Table S3. of Skewing in Arabidopsis roots involves disparate environmental signaling pathways

description: Comparing Col-0 to WS at different growth angles. (XLS 103 kb)
DOI: 10.6084/m9.figshare.c.3679057_d2.v1
title: Additional file 3: of Skewing in Arabidopsis roots involves disparate environmental signaling pathways

description: Validation of microarray data using qRT-PCR. The quantitative RT-PCR data for the genes encoding SEN1, ASN1, HKT1, MIOX4, SIS, SWEET11 and DINare provided numerically in a spread sheet. (XLS 12 kb)
DOI: 10.6084/m9.figshare.c.3679057_d2
title: Additional file 3: of Skewing in Arabidopsis roots involves disparate environmental signaling pathways

description: Validation of microarray data using qRT-PCR. The quantitative RT-PCR data for the genes encoding SEN1, ASN1, HKT1, MIOX4, SIS, SWEET11 and DINare provided numerically in a spread sheet. (XLS 12 kb)
DOI: 10.6084/m9.figshare.c.3680575_d3
title: Additional file 1: of A novel statistical approach for identification of the master regulator transcription factor

description: Test Dataset. This file contains an example test dataset where our method can be implemented. This simulated data contains 10 transcription factors, namely TF 1, TF 2, …, TF 10 along with 105 genes that were regulated by these transcription factors. Among the transcription factors, TF 1 was generated to play the role of the master regulator. (CSV 1382 kb)
DOI: 10.6084/m9.figshare.c.3680575_d3.v1
title: Additional file 1: of A novel statistical approach for identification of the master regulator transcription factor

description: Test Dataset. This file contains an example test dataset where our method can be implemented. This simulated data contains 10 transcription factors, namely TF 1, TF 2, …, TF 10 along with 105 genes that were regulated by these transcription factors. Among the transcription factors, TF 1 was generated to play the role of the master regulator. (CSV 1382 kb)
DOI: 10.6084/m9.figshare.c.3680578_d2.v1
title: Additional file 1: Table S1. of Spatial and temporal distribution of house infestation by Triatoma infestans in the Toro Toro municipality, Potosi, Bolivia

description: Number of localities evaluated once or twice a year during the study period. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3680578_d3
title: Additional file 2: Table S2. of Spatial and temporal distribution of house infestation by Triatoma infestans in the Toro Toro municipality, Potosi, Bolivia

description: Number of evaluated houses varied within and between years. (XLS 19 kb)
DOI: 10.6084/m9.figshare.c.3680578_d2
title: Additional file 1: Table S1. of Spatial and temporal distribution of house infestation by Triatoma infestans in the Toro Toro municipality, Potosi, Bolivia

description: Number of localities evaluated once or twice a year during the study period. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3681943_d3
title: Additional file 1: of Musculoskeletal disorders as underlying cause of death in 58 countries, 1986â  2011: trend analysis of WHO mortality database

description: Excel file including all supplementary tables. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3681943_d3.v1
title: Additional file 1: of Musculoskeletal disorders as underlying cause of death in 58 countries, 1986â  2011: trend analysis of WHO mortality database

description: Excel file including all supplementary tables. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3683068_d1.v1
title: Additional file 4: Table S4. of Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India

description: Spreadsheet showing list of all unique differentially methylated probes. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.c.3683068_d1
title: Additional file 4: Table S4. of Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India

description: Spreadsheet showing list of all unique differentially methylated probes. (XLSX 23 kb)
DOI: 10.15468/dl.wmree9
title: Occurrence Download

description: A dataset containing 68 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Saussurea obvallata (DC.) Edgew., 1846"
 ]
}

 The dataset includes 68 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038636-241126133413365/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.3684199_d3.v1
title: Additional file 3: Table S1. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts

description: YGOB data set analysis, including dN/dS data, likelihood-ratio tests' results, and S. cerevisiae protein properties and functions for 535 orthogroups. (XLSX 242Â kb)
DOI: 10.15468/dl.gxq4t3
title: Occurrence Download

description: A dataset containing 136 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Azolla pinnata subsp. asiatica R.M.K.Saunders & K.Fowler"
 ]
}

 The dataset includes 136 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038637-241126133413365/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.3684199_d3
title: Additional file 3: Table S1. of Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts

description: YGOB data set analysis, including dN/dS data, likelihood-ratio tests' results, and S. cerevisiae protein properties and functions for 535 orthogroups. (XLSX 242Â kb)
DOI: 10.6084/m9.figshare.c.3684211_d3.v1
title: Additional file 18: R code. of Evaluation of logistic regression models and effect of covariates for caseâ  control study in RNA-Seq analysis

description: This R code regenerates the simulated data sets. (R 6 kb)
DOI: 10.6084/m9.figshare.c.3684316_d2
title: Additional file 5: of Mechanism of action of trabectedin in desmoplastic small round cell tumor cells

description: Pathway analysis after trabectedin treatment of JN-DSRCT-1 cells. Pathway analysis for the differentially expressed genes 6 h after trabectedin wash-out. pSize, number of genes belonging to the pathway; tA, statistical measurement of pathway activation (if greater than 0) or inhibition (if lower than 0), pGFdr, FDR adjusted p-value. (XLSX 39 kb)
DOI: 10.6084/m9.figshare.c.3684331_d2.v1
title: MOESM2 of Testing the potential significance of different scion/rootstock genotype combinations on the ecology of old cultivated olive trees in the southeast Mediterranean area

description: Additional file 2: Table S1. Quantitative phenotypic data for each tree belonging to GG1 and GG2; md represent missing data.
DOI: 10.6084/m9.figshare.c.3684331_d2
title: MOESM2 of Testing the potential significance of different scion/rootstock genotype combinations on the ecology of old cultivated olive trees in the southeast Mediterranean area

description: Additional file 2: Table S1. Quantitative phenotypic data for each tree belonging to GG1 and GG2; md represent missing data.
DOI: 10.6084/m9.figshare.c.3684340_d1.v1
title: Additional file 6: of 
                     De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages

description: Alignment of GSTF1 protein sequences from Apera and Alopecurus. (RTF 159 kb)
DOI: 10.6084/m9.figshare.c.3684340_d1
title: Additional file 6: of 
                     De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages

description: Alignment of GSTF1 protein sequences from Apera and Alopecurus. (RTF 159 kb)
DOI: 10.6084/m9.figshare.c.3684343_d1
title: Additional file 2: of Markov State Models of gene regulatory networks

description: Contains the scripts used to produce the figures and tables. (ZIP 76Â kb)
DOI: 10.6084/m9.figshare.c.3684316_d5.v1
title: Additional file 2: of Mechanism of action of trabectedin in desmoplastic small round cell tumor cells

description: RT-Q-PCR primers. Table of RT-Q-PCR primers used. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.c.3684355_d1.v1
title: MOESM1 of Comparative genomic analysis of Shiga toxin-producing and non-Shiga toxin-producing Escherichia coli O157 isolated from outbreaks in Korea

description: Additional file 1: Table S1. Selected genes from NCCP15739 and NCCP15738 for functional annotation clustering.
DOI: 10.5281/zenodo.14216336
title: Sustainable Agricultural Pathways in Europe (SIPATH) – land use data

description: The published land use data were part of the project “What is Sustainable Intensification? Operationalizing Sustainable Agricultural Pathways in Europe (SIPATH)”, which was funded by the Swiss National Science Foundation (grant no. CRSII5_183493). The overall objective of this project was to assess short-term trajectories in agriculture land use and landscape structure over a period of 20 years for 16 individual study sites located in 11 countries, ranging from the Mediterranean to the boreal zone. The following datasets illustrate land use data that were generated for the different study sites at two points in time between 2000 and 2020, depending on data availability. The data collection process encompassed land use mapping through visual image interpretation of orthorectified aerial photographs using geographic information systems (ESRI ArcGIS Pro). Land use digitalization was conducted by two scientists in Switzerland, who were in contact with the respective project partners in the study countries to exchange expert knowledge. Minimal mapping unit was 25m2 for areal elements. Land cover was classified following the European Nature Information System (EUNIS) habitat classification (EEA 2019). The broadest habitat classes were systematically mapped in the study sites, with each covering an area of approximately 25 km². While EUNIS focuses on habitat types, the study, however, targeted the intensity of agricultural land-use, several EUNIS classes were complemented with levels of land-use intensities. This was applied for grassland, olive groves and fruit orchards. The spatial resolution of the orthophotos ranged from 25cm to 2m. Accordingly, there were situations in which the spatial resolution was insufficient to accurately determine the land use. In such cases, either orthophotos from about the same year were consulted, possibly showing different phenological stages, or land use statistics and expert judgement based on local expert knowledge of the respective study area were applied.

 

Reference:

EEA, 2019. EUNIS habitat classification 2007 (Revised descriptions 2012) amended 2019. Copenhagen (Permalink)
DOI: 10.5281/zenodo.14216337
title: Sustainable Agricultural Pathways in Europe (SIPATH) – land use data

description: The published land use data were part of the project “What is Sustainable Intensification? Operationalizing Sustainable Agricultural Pathways in Europe (SIPATH)”, which was funded by the Swiss National Science Foundation (grant no. CRSII5_183493). The overall objective of this project was to assess short-term trajectories in agriculture land use and landscape structure over a period of 20 years for 16 individual study sites located in 11 countries, ranging from the Mediterranean to the boreal zone. The following datasets illustrate land use data that were generated for the different study sites at two points in time between 2000 and 2020, depending on data availability. The data collection process encompassed land use mapping through visual image interpretation of orthorectified aerial photographs using geographic information systems (ESRI ArcGIS Pro). Land use digitalization was conducted by two scientists in Switzerland, who were in contact with the respective project partners in the study countries to exchange expert knowledge. Minimal mapping unit was 25m2 for areal elements. Land cover was classified following the European Nature Information System (EUNIS) habitat classification (EEA 2019). The broadest habitat classes were systematically mapped in the study sites, with each covering an area of approximately 25 km². While EUNIS focuses on habitat types, the study, however, targeted the intensity of agricultural land-use, several EUNIS classes were complemented with levels of land-use intensities. This was applied for grassland, olive groves and fruit orchards. The spatial resolution of the orthophotos ranged from 25cm to 2m. Accordingly, there were situations in which the spatial resolution was insufficient to accurately determine the land use. In such cases, either orthophotos from about the same year were consulted, possibly showing different phenological stages, or land use statistics and expert judgement based on local expert knowledge of the respective study area were applied.

 

Reference:

EEA, 2019. EUNIS habitat classification 2007 (Revised descriptions 2012) amended 2019. Copenhagen (Permalink)
DOI: 10.6084/m9.figshare.c.3685348_d4
title: Additional file 1: Table S1. of Evolutionary analysis of the SUB1 locus across the Oryza genomes

description: SUB1-like genes identified in Oryza species. (XLSX 22 kb)
DOI: 10.15468/dl.m6mzer
title: Occurrence Download

description: A dataset containing 9981 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON((48.26831 -18.75732,48.75659 -18.75732,48.75659 -17.86654,48.26831 -17.86654,48.26831 -18.75732))"
 ]
}

 The dataset includes 9981 records from 96 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038638-241126133413365/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.3686692_d6.v1
title: Additional file 6: of Comparative genomics of canine hemoglobin genes reveals primacy of beta subunit delta in adult carnivores

description: Taxonomy annotation of genes used for the phylogenetic analysis with identification number and species information. (XLSX 15Â kb)
DOI: 10.15468/dl.stpf9r
title: Occurrence Download

description: A dataset containing 4559565 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Australia",
 "TaxonKey is Mammalia"
 ]
}

 The dataset includes 4559565 records from 363 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038626-241126133413365/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.3688297_d1.v1
title: Additional file 1: of Language background in early life may be related to neuropsychiatry symptoms in patients with Alzheimer disease

description: All the statistic results of this study can be calculated from our additional file 1 (XLS 368Â kb)
DOI: 10.6084/m9.figshare.c.3688297_d1
title: Additional file 1: of Language background in early life may be related to neuropsychiatry symptoms in patients with Alzheimer disease

description: All the statistic results of this study can be calculated from our additional file 1 (XLS 368Â kb)
DOI: 10.6084/m9.figshare.c.3688291_d3.v1
title: Additional file 2: of SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence

description: Values of the epitope/non-epitope energy-like feature F9. (ZIP 61 kb)
DOI: 10.6084/m9.figshare.c.3688291_d3
title: Additional file 2: of SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence

description: Values of the epitope/non-epitope energy-like feature F9. (ZIP 61 kb)
DOI: 10.6084/m9.figshare.c.3688291_d4.v1
title: Additional file 3: of SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence

description: Values of the solvent accessibility energy-like feature F11. (ZIP 129 kb)
DOI: 10.6084/m9.figshare.c.3688303_d2.v1
title: Additional file 2: of Towards an optimal therapy strategy for myogenous TMD, physiotherapy compared with occlusal splint therapy in an RCT with therapy-and-patient-specific treatment durations

description: Dataset. Dataset related to Tables 1-4. (XLSX 1434 kb)
DOI: 10.6084/m9.figshare.c.3688291_d4
title: Additional file 3: of SEPIa, a knowledge-driven algorithm for predicting conformational B-cell epitopes from the amino acid sequence

description: Values of the solvent accessibility energy-like feature F11. (ZIP 129 kb)
DOI: 10.6084/m9.figshare.c.3688303_d2
title: Additional file 2: of Towards an optimal therapy strategy for myogenous TMD, physiotherapy compared with occlusal splint therapy in an RCT with therapy-and-patient-specific treatment durations

description: Dataset. Dataset related to Tables 1-4. (XLSX 1434 kb)
DOI: 10.5281/zenodo.14511637
title: MAKANAN TRADISIONAL HALUA SUKU MELAYU SEBAGAI DAYA TAYA TARIK WISATA KULINER DI KABUPATEN LANGKAT
title: Makanan khas halus

description: Traditional Food, Malay Traditonal Food, Tourist Attraction
DOI: 10.5281/zenodo.14511638
title: MAKANAN TRADISIONAL HALUA SUKU MELAYU SEBAGAI DAYA TAYA TARIK WISATA KULINER DI KABUPATEN LANGKAT
title: Makanan khas halus

description: Traditional Food, Malay Traditonal Food, Tourist Attraction
DOI: 10.6084/m9.figshare.c.3689179_d3
title: Additional file 7: of The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes

description: 16S gene alignments in FASTA format. (TXT 38Â kb)
DOI: 10.6084/m9.figshare.c.3689179_d4.v1
title: Additional file 1: of The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes

description: Statistical model estimations and results. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.c.3689182_d2.v1
title: Additional file 1 of VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces

description: Dated species tree used in the example analysis that yielded the traces in Additional files 2 and 3. (TXT 866 KB)
DOI: 10.6084/m9.figshare.c.3689182_d2
title: Additional file 1 of VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces

description: Dated species tree used in the example analysis that yielded the traces in Additional files 2 and 3. (TXT 866 KB)
DOI: 10.6084/m9.figshare.c.3689179_d4
title: Additional file 1: of The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes

description: Statistical model estimations and results. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.c.3689179_d7.v1
title: Additional file 6: of The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes

description: Dataset containing all data used in the statistical models together with the strains IDâ  s and accession numbers. (XLSX 196Â kb)
DOI: 10.6084/m9.figshare.c.3690615_d1
title: Additional file 1: of Cardiorenal Anemia Syndrome and Survival among Heart Failure Patients in Tanzania: A Prospective Cohort Study

description: CRAS study Tanzania - dataset. (XLSX 155 kb)
DOI: 10.6084/m9.figshare.c.3690579_d18.v1
title: Additional file 19: of Anopheline salivary protein genes and gene families: an evolutionary overview after the whole genome sequence of sixteen Anopheles species

description: Peptide sequences in fasta format. This file includes the amino acid sequences of the 824 anopheline salivary proteins analyzed in this study and included in Additional file 2 (excel spreadsheet). The file is in fasta format (.fas) and can be viewed with a text editor. (FAS 266Â kb)