cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3612413_d7.v1
title: Additional file 5: Table S2. of A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large

description: All proteins identified, organized by bait protein. (XLSX 140 kb)
DOI: 10.6084/m9.figshare.c.3612419_d5.v1
title: Additional file 10: of Genetic association and stress mediated down-regulation in trabecular meshwork implicates MPP7 as a novel candidate gene in primary open angle glaucoma

description: Contains table representing association data of all SNPs showing suggestive association (pâ
DOI: 10.6084/m9.figshare.c.3612443_d2.v1
title: Additional file 3: Table S3. of Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

description: Coverage of PAO1 by the metagenomes, coverage with &gt;3 reads per position and phred score &gt;30. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.c.3612443_d3.v1
title: Additional file 5: Table S5. of Is genotyping of single isolates sufficient for population structure analysis of Pseudomonas aeruginosa in cystic fibrosis airways?

description: Detailed overview of SNPs found in single isolates and the rediscovery in the metagenomic reads. For each isolate it is indicated whether the mutation has been discovered or not, indicated by 1 and 0 respectively. For each metagenome the percentage of reads (%) representing the SNP found in the single isolates are shown together with the actual number of reads that have been called for each base, C, G, A, and T. For the metagenome(s) it is indicated at the bottom of the column the number of SNPs rediscovered in &gt;10, 50 and 90Â % of the metagenomic reads, as well as the total number of SNPs covered by the metagenomic reads. (XLSX 239 kb)
DOI: 10.34740/kaggle/dsv/10222981
title: Top Universities - QS Asian Rankings 2024
DOI: 10.6084/m9.figshare.c.3612509_d1.v1
title: Additional file 14: Table S2. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: Chimeras removed from dataset B3. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.c.3612509_d3.v1
title: Additional file 9: Figure S8. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. Spike-in retrieval as a function of number of positive samples, by dataset size. Aggregated results across 150 iterations of multiplicative spike-ins of magnitude 5 with 50% cases, in datasets A1, A1s, and A1m. Each dot represents a spiked OTU. The Y-axis displays its p value quantile (0 is lowest p value, 1 is highest p value) within that DA run, and the X axis shows how many samples are positive (nonzero) for that OTU. Results from the three datasets are overlaid with different colors and faceted by statistical method. B. Spike-in retrieval as a function of number of positive samples, by case proportion. Aggregated results across 150 iterations of multiplicative spike-ins of magnitude 5 with 10, 25, or 50% cases, in dataset A1. Each dot represents a spiked OTU. The Y-axis displays its p value quantile (0 is lowest p value, 1 is highest p value) within that DA run, and the X axis shows how many samples are positive (nonzero) for that OTU. Results from the three case proportions are overlaid with different colors, and faceted by statistical method. C. Spike-in retrieval as a function of number of positive samples, by spike-in magnitude. Aggregated results across 150 iterations of multiplicative spike-ins of magnitudes 0.5, 2, 5, 10, and 20 with 50% cases, in dataset A1. Each dot represents a spiked OTU. The Y-axis displays its p value quantile (0 is lowest p value, 1 is highest p value) within that DA run, and the X axis shows how many samples are positive (nonzero) for that OTU. Results from the different spike-in magnitudes are overlaid with different colors, and faceted by statistical method. (ZIP 16398 kb)
DOI: 10.6084/m9.figshare.c.3612518_d1.v1
title: Additional file 1: Table S1. of Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation

description: Sequencing statistics summary. Table S2. Genome feature association of filtered variant-removed CpGs for adipose and blood. Table S3. Characteristics of unmethylated (UMR) and low-methylated regions (LMR) in adipose and blood. Table S4. Number of invariable sites in filtered datasets at various minimum coverages. Table S5. pDMR statistics in adipose and blood. Table S6. Result of the TFBS motif analysis using the HOMER software. Table S7. MZ2 vs. MZ3-derived significant DMCs overlapping known smoking methylation loci. Table S8. Genetic and non-genetic effect of CpG methylation. Table S9. Overall detected CpH methylation per tissue and strand. (XLSX 56 kb)
DOI: 10.6084/m9.figshare.c.3612509_d11.v1
title: Additional file 5: Figure S4. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. Area under the curve distributions for additive spike-ins in dataset A1. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A1, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. B. Area under the curve distributions for additive spike-ins in dataset A2. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A2, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. C. Area under the curve distributions for additive spike-ins in dataset A3. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A3, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. (ZIP 2183 kb)
DOI: 10.6084/m9.figshare.c.3612509_d12.v1
title: Additional file 4: Figure S3. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. Area under the curve distributions for multiplicative spike-ins in dataset A1. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A1, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. B. Area under the curve distributions for multiplicative spike-ins in dataset A2. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A2, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. C. Area under the curve distributions for multiplicative spike-ins in dataset A3. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of spike-in magnitude and case proportion (vertical panels) in dataset A3, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. (ZIP 2685 kb)
DOI: 10.6084/m9.figshare.c.3612509_d13.v1
title: Additional file 3: Figure S2. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. False positive rate distributions for datasets A1–A3. Violin plot of distributions of false positive rate (FPR) in 150 iterations for each case proportion in datasets A1–A3 (vertical panels), analyzed with all differential relative abundance methods (horizontal panels). FPR is defined as the fraction of OTUs with p
DOI: 10.6084/m9.figshare.c.3612509_d14.v1
title: Additional file 8: Figure S7. of Large-scale benchmarking reveals false discoveries and count transformation sensitivity in 16S rRNA gene amplicon data analysis methods used in microbiome studies

description: A. Area under the curve distributions for multiplicative spike-ins in dataset A4. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of multiplicative spike-in magnitude and case proportion (vertical panels) in dataset A4, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. B. Area under the curve distributions for additive spike-ins in dataset A4. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each combination of additive spike-in magnitude and case proportion (vertical panels) in dataset A4, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. C. Area under the curve distributions for mixed multiplicative spike-ins in dataset A4. Violin plot of distributions of area under the receiver operating characteristic curve (AUC) for spiked vs non-spiked p values from differential relative abundance (DA) tests. AUC distributions from 150 iterations for each case proportion (vertical panels) in dataset A4, analyzed with all differential relative abundance methods (horizontal panels). Black dots represent medians in each distribution. (ZIP 1831 kb)
DOI: 10.6084/m9.figshare.c.3612566_d1.v1
title: Additional file 2: Table S2. of Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors

description: CTR-NT Differentially regulated genes. Breakdown of genes differentially up and downregulated with â Ľ1.5 fold change in CTR-NT blastocyst compared to in vitro fertilized embryos. Red and green colors represent up and downregulation, respectively. (XLS 261Â kb)
DOI: 10.6084/m9.figshare.c.3612593_d2.v1
title: Additional file 2: Table S1. of Genome-wide analysis and expression profiling of glyoxalase gene families in soybean (Glycine max) indicate their development and abiotic stress specific response

description: Pairwise identities between paralogous pairs of GLYI proteins from Soybean. Table S2. Percentage of identities between all GLYII proteins from Soybean. Table S5. Expression analysis of soybean GLYI and GLYII genes through RNA-seq data (XLS 40Â kb)
DOI: 10.6084/m9.figshare.c.3612617_d1.v1
title: Additional file 6: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The interspecific Tajimaâ  s D values of TFBS, coding sequences (CDS) and introns. (XLS 1229 kb)
DOI: 10.6084/m9.figshare.c.3612617_d2.v1
title: Additional file 3: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The predicted transcription factor binding sites (TFBSs) in the promoters of genes in the pathways of photoperiod, vernalization and pathway integration in Arabidopsis, Brachypodium, wheat and barley. (XLSX 406 kb)
DOI: 10.6084/m9.figshare.c.3612617_d3.v1
title: Additional file 5: of Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

description: The intraspecific Tajimaâ  s D values of TFBSs in Arabidopsis, Brachypodium, wheat and barley. (XLS 110 kb)
DOI: 10.25828/19gv-s240
title: Labour Market Dynamics in South Africa 2022
DOI: 10.25451/flinders.28043723
title: Data

description: There are 2 processed Excel files and 19 raw JSON files
DOI: 10.25451/flinders.28043723.v1
title: Data

description: There are 2 processed Excel files and 19 raw JSON files
DOI: 10.5281/zenodo.14215089
title: X-SPIM light sheet volumetric dataset with two illumination and two detection sides of an 3-dpf H2B:GFP zebrafish embryo

description: This dataset encompasses four views from two illumination and two detection sides using an X-SPIM home-build light sheet microscope in Prof. Jan Huisken's lab (Multiscale Biology, Göttingen, Germany). A Toptica iChrome CLE fibre-coupled laser, Nikon water immersion lenses with 10x/0.3 as illumination and detection lenses, Physik Instrumente (PI) compact linear stages for sample positioning and a PCO pco.panda sCMOS camera to collect the fluorescence signal, were used to acquire volumetric stacks (488 nm excitation, band-pass 525/50 nm emission filter, 25 ms exposure time, 40 frames/s, 2.5 µm z-steps).
DOI: 10.5281/zenodo.14215090
title: X-SPIM light sheet volumetric dataset with two illumination and two detection sides of an 3-dpf H2B:GFP zebrafish embryo

description: This dataset encompasses four views from two illumination and two detection sides using an X-SPIM home-build light sheet microscope in Prof. Jan Huisken's lab (Multiscale Biology, Göttingen, Germany). A Toptica iChrome CLE fibre-coupled laser, Nikon water immersion lenses with 10x/0.3 as illumination and detection lenses, Physik Instrumente (PI) compact linear stages for sample positioning and a PCO pco.panda sCMOS camera to collect the fluorescence signal, were used to acquire volumetric stacks (488 nm excitation, band-pass 525/50 nm emission filter, 25 ms exposure time, 40 frames/s, 2.5 µm z-steps).
DOI: 10.6084/m9.figshare.c.3612668_d1.v1
title: Additional file 1: of Parallel study about the effects of psychotherapy on patients with dental phobia determined by anxiety scores and saliva secretion and composition

description: Statistik Zahnarztphobie 2015-01-18.(XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3612671_d3.v1
title: Additional file 3. of Cleansing effect of acidic L-arginine on human oral biofilm

description: Summary of percent abundance of salivary microbiota from healthy volunteers. (XLS 48 kb)
DOI: 10.6084/m9.figshare.c.3612710_d3.v1
title: Additional file 2: Table S14. of Metabolic requirements for cancer cell proliferation

description: Flux distributions generated from metformin treatment simulations. Baseline (total carbon uptake minimized, NNT present, GDH reversible); NNT absent, GDH reversible; NNT absent, GDH irreversible; NNT present, GDH irreversible; and total glutamine uptake minimized cases all provided. (XLSX 50 kb)
DOI: 10.6084/m9.figshare.c.3612740_d1.v1
title: Additional file 1: Table S1. of Proteomic and Glycomic Characterization of Rice Chalky Grains Produced Under Moderate and High-temperature Conditions in Field System

description: Proteomic comparison of chalky and perfect grains harvested in 2009 and 2010. s.d., standard deviation; # AAs, the number of amino acids; MW, the calculated molecular weight; pI, the calculated isoelectric point; ÎŁCoverage, the percentage of sequence coverage. (XLSX 62343Â kb)
DOI: 10.15468/dl.p5k333
title: Occurrence Download

description: A dataset containing 21814 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is 2001-2019 The Marine Biological Association of the UK (MBA) Shore Thing Survey"
 ]
}

 The dataset includes 21814 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037550-241126133413365/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.3612743_d1.v1
title: Additional file 1: of The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

description: Supplementary tables. (XLSX 148 kb)
DOI: 10.6084/m9.figshare.c.3612815_d1.v1
title: Additional file 7: Table S6. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Overlap between detected putative L1 ASP transcripts from Table S1 and genes identified to play a causal role in cancer (COSMIC database). (XLSX 18 kb)
DOI: 10.6084/m9.figshare.c.3612815_d2.v1
title: Additional file 9: Table S8. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Summary of mouse ESTs (mm10) supporting putative L1 ASP transcripts. Filtering eliminated many putative ESTs because unlike human ESTs much fewer mouse ESTs are labelled with transcript direction information within the intronOrientation field. The 307 ESTs represented in the table sometimes overlap more than one gene and may be represented more than once. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3612815_d3.v1
title: Additional file 4: Table S3. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Peptide identification for ESTs in Table S1 using Transdecoder. Putative predicted peptides were characterized for the presence of a stop codon and the ORF0 open reading frame. (XLSX 197 kb)
DOI: 10.15468/dl.rfjxp2
title: Occurrence Download

description: A dataset containing 542 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-21.56854 25.90162,91.56854 25.90162,91.56854 71.09838,-21.56854 71.09838,-21.56854 25.90162))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lasius neglectus Van Loon, Boomsma & Andrasfalvy, 1990"
 ]
}

 The dataset includes 542 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037551-241126133413365/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.3612815_d4.v1
title: Additional file 1: Table S1. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Summary of genomic screen result identifying ESTs supporting putative L1 antisense promoter (ASP) transcripts in the human genome (hg19). The 2015 ESTs are sometimes represented more than once in Table S1 because a single EST can overlap multiple cognate genes. (XLSX 276 kb)
DOI: 10.6084/m9.figshare.c.3612815_d5.v1
title: Additional file 8: Table S7. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Summary of ESTs supporting putative L1 ASP transcript where an independent EST supported L1 exonization. These L1 ASP transcripts are considered to be potentially explained by L1 exonization and are of lower confidence. (XLSX 187 kb)
DOI: 10.6084/m9.figshare.c.3612815_d6.v1
title: Additional file 10: Table S9. of Genome-wide characterization of human L1 antisense promoter-driven transcripts

description: (excel) Summary of publicly available data used for L1 ASP analysis. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3612833_d1.v1
title: Additional file 2: of A phase I clinical study of immunotherapy for advanced colorectal cancers using carcinoembryonic antigen-pulsed dendritic cells mixed with tetanus toxoid and subsequent IL-2 treatment

description: The results of T cell proliferation assay. (XLS 93Â kb)
DOI: 10.6084/m9.figshare.c.3612839_d6.v1
title: Additional file 2: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the BSI-53 in the Ukrainian general population: factor loadings. Results of confirmatory factor analysis. Factor loadings for nine dimensions of the BSI-53 in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 11Â kb)
DOI: 10.6084/m9.figshare.c.3612848_d2.v1
title: Additional file 6: Table S2. of MicroRNA-derived network analysis of differentially methylated genes in schizophrenia, implicating GABA receptor B1 [GABBR1] and protein kinase B [AKT1]

description: The number of different transcription factor-binding sites for 15 GABBR1-related genes (binding partners and neighborhood genes of GABBR1 in Fig.Â 3) mapped to the cis regulatory elements as identified by Thurman et al. [40] based on the compilation of all TFBSs in the human genome by [41]. (XLSB 58 kb)
DOI: 10.6084/m9.figshare.c.3612839_d7.v1
title: Additional file 4: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the BSI-18 in the Ukrainian general population: factor loadings. Results of confirmatory factor analysis. Factor loadings for three dimensions of the BSI-18 in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3612839_d8.v1
title: Additional file 5: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the SCL-14 in the Ukrainian general population: factor loadings. Results of confirmatory factor analysis. Factor loadings for three dimensions of the SCL-14 in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3612848_d4.v1
title: Additional file 2: Table S1. of MicroRNA-derived network analysis of differentially methylated genes in schizophrenia, implicating GABA receptor B1 [GABBR1] and protein kinase B [AKT1]

description: All experimentally verified targets that were found differentially methylated in schizophrenics by Wockner et al. [6] (in promoters overlapping a CpG island) of all microRNAs associated with schizophrenia. The number of promoter and cis elements associated with each gene as found by Thurman et al. [40] are shown in columns 2 and 3, respectively. (XLSB 247 kb)
DOI: 10.6084/m9.figshare.c.3612839_d9.v1
title: Additional file 1: of Validity assessment of the symptom checklist SCL-90-R and shortened versions for the general population in Ukraine

description: Confirmatory factor analysis of the SCL-90-R in the Ukrainian general population: factor loadings. Results of confirmatory factor analysis. Factor loadings for nine dimensions of the SCL-90-R in 1997, 1999 and 2014 studies that are representative of the Ukrainian population. (XLSX 12Â kb)