cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.27290031.v2
title: Metadata

description: The SARS-CoV-2 induced disease, COVID-19 is a worldwide public health concern with a rapid transmission, pathogenicity, and mortality rate. To elucidate the viral mutational changes and screen the emergence of new variants of concern, we conducted this study in Bangladesh. The viral RNA genome was sequenced using Illumina COVID Seq protocol and genomic data processing and evaluation was performed in DRAGEN COVID Lineage software. Variant analysis revealed that the number of Delta, Omicron, and Mauritius variants identified were 88%, 8%, and 4%, respectively. All of the 25 samples had 23403A&gt;G (D614G, S gene), 3037 C&gt;T (nsp3), and 14408 C&gt;T (nsp12) mutations, where 23403 A&gt;G was responsible for increased transmission. Omicron had the highest number of unique mutations in spike protein (i.e., substitutions, deletions, and insertions) which may explain its more transmissibility and immune evading ability than Delta. A total of 779 mutations were identified where 691 substitution, 85 deletion, and 3 insertion mutations were observed. To sum up, our study will enrich the genomic database of SARS-CoV-2, aiding treatment strategy and understanding the virus’s preferences in both mutation type and site for predicting newly emerged virus’s survival strategy and thus for being prepared to counteract them.
DOI: 10.6084/m9.figshare.c.3600710_d1.v1
title: Additional file 3: of Unappreciated diversification of stem archosaurs during the Middle Triassic predated the dominance of dinosaurs

description: Supertree topology with phytosaurs as crown group and stem group archosaurs. (NEX 20 kb)
DOI: 10.6084/m9.figshare.c.3600707_d5.v1
title: MOESM3 of The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies

description: Additional file 3. Memory and time requirements of the ExonMatchSolver on simulated data. The raw data is provided as Addtional_file3.xlsx. Raw data on memory and time assessment of the ExonMatchSolver on simulated data. The memory and time requirements of the ExonMatchSolver were measured for different numbers of exons (1, 3, 5, 7, 10, 12, 50, 70, 100) and paralogs (4, 6, 8 10, 20. 40, 70, 100) on data simulated with ALF. Memory was estimated as Resident Set Size. Memory and running time were sampled for each combination of paralogs and exons for 20 independent runs of fragmentation and averaged.
DOI: 10.6084/m9.figshare.c.3600710_d3.v1
title: Additional file 2: of Unappreciated diversification of stem archosaurs during the Middle Triassic predated the dominance of dinosaurs

description: MorphoJ data set. (TXT 10497 kb)
DOI: 10.21227/3722-mg37
title: Dig21000

description: Dig21000 is a comprehensive dataset consisting of 21,000 images of digit-based rotary meters photographed in uncontrolled environments. It integrates images from open datasets on the Roboflow platform and those independently collected. After undergoing cleaning, the images are randomly divided into training and testing sets at a ratio of 6:1. It contains 10 digit categories. The images are affected by multiple factors and can be used for research on digital dial recognition. It is publicly available and citation is required when using it.
DOI: 10.6084/m9.figshare.c.3600773_d2.v1
title: Additional file 6 of Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities

description: Pathway enrichment analysis for non-immune diseases. This Excel file contains hypergeometric test p values per pathway per disease for KEGG, BioCarta, Reactome, and PID pathway collections as well as all canonical pathway gene sets collected from MSigDB version 4.0, and Fisherâ  s combined p values for ASD and its co-morbidities excluding the immune-related diseases: bacterial and viral infection, asthma, inflammatory bowel disease, upper respiratory infection, and ear infection. (XLS 673 kb)
DOI: 10.6084/m9.figshare.c.3600764_d2.v1
title: Additional file 8: Table E4. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: MADAD – Ingenuity Pathway Analysis. (XLSX 33 kb)
DOI: 10.20363/zfmk-coll.mantodea-2024-12
title: ZFMK Mantodea collection

description: The Mantodea collection at the Leibniz Institute for the Analysis of Biodiversity Change (LIB) - Museum Koenig Bonn contains large parts of the collection of Johann Klapperich as well as the collection of A. Schoop and the permanent loan of the Zoo Cologne
DOI: 10.6084/m9.figshare.28041254
title: TPNet_code

description: This repository contains the pre-trained TPNet model (TPNet.pth), developed using the PyTorch framework, along with demo code (TPNet.py) to guide the estimation of near-surface Total Phosphorus (TP) concentration from Landsat surface reflectance using TPNet. For any questions or issues regarding the use of this model, or suggestions for improving TPNet, please contact Hongwei Guo at ghwxzsy@163.com.
DOI: 10.6084/m9.figshare.28041254.v1
title: TPNet_code

description: This repository contains the pre-trained TPNet model (TPNet.pth), developed using the PyTorch framework, along with demo code (TPNet.py) to guide the estimation of near-surface Total Phosphorus (TP) concentration from Landsat surface reflectance using TPNet. For any questions or issues regarding the use of this model, or suggestions for improving TPNet, please contact Hongwei Guo at ghwxzsy@163.com.
DOI: 10.6084/m9.figshare.c.3600764_d3.v1
title: Additional file 13: Table E8. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: Overrepresented Hub30 Genes and module names. (NL) (XLSX 47Â kb)
DOI: 10.6084/m9.figshare.c.3600773_d5.v1
title: Additional file 5 of Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities

description: Posterior probability analysis. This Excel file contains the minimum Bayes factors and minimum posterior probabilities for null hypotheses for the significant KEGG pathways. It also contains the 100 pathway p value distributions generated by permuting the null data set. Finally, it has Fisherâ  s combined p values for ASD and its co-morbidities with the null p value distribution (one sheet per disease). (XLSX 380 kb)
DOI: 10.6084/m9.figshare.c.3600773_d6.v1
title: Additional file 4 of Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities

description: Pathway enrichment analysis. This Excel file contains hypergeometric test p values per pathway per disease for KEGG, BioCarta, Reactome, and PID pathway collections as well as all canonical pathway gene sets collected from MSigDB version 4.0., and Fisherâ  s combined p values for ASD and its co-morbidities. (XLS 1444 kb)
DOI: 10.6084/m9.figshare.c.3600785_d1.v1
title: Additional file 4: of ROR2 is epigenetically inactivated in the early stages of colorectal neoplasia and is associated with proliferation and migration

description: Table of qRT-PCR Primer Sequences. List of qRT-PCR primer sequences used in experimentation. (TXT 726 bytes)
DOI: 10.6084/m9.figshare.c.3600764_d4.v1
title: Additional file 17: Table E12. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: BH adjusted p-values WGCNA NL Modules. (XLSX 9Â kb)
DOI: 10.15468/dl.zf5zwu
title: Occurrence Download

description: A dataset containing 3580 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-7.86003 35.72844,0.34047 35.72844,0.34047 40.04353,-7.86003 40.04353,-7.86003 35.72844))",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "TaxonKey is Cyprinus carpio Linnaeus, 1758"
 ]
}

 The dataset includes 3580 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037515-241126133413365/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.3600785_d4.v1
title: Additional file 3: of ROR2 is epigenetically inactivated in the early stages of colorectal neoplasia and is associated with proliferation and migration

description: Table of qRT-PCR Primer Sequences. Histopathological information on adenoma samples and matching normal mucosa. Age ranges of patients 57â  79. Samples listed in order from top to bottom in FigÂ 2F. (TXT 552 bytes)
DOI: 10.6084/m9.figshare.c.3600797_d1.v1
title: Additional file 1: of GFRA3 promoter methylation may be associated with decreased postoperative survival in gastric cancer

description: Î˛ values for selected CpG-sites. (TXT 7 kb)
DOI: 10.6084/m9.figshare.c.3600764_d9.v1
title: Additional file 5: Table E2. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: Consensus of re-analyized included datasets (by Probes). (XLSX 60Â kb)
DOI: 10.6084/m9.figshare.c.3600812_d6.v1
title: Additional file 1: Table S1. of Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant

description: Cluster analysis showing fold change values and description of assembled transcripts of SRA database generated from N. benthamiana leaf discs exposed to oxalic acid (20Â mM) for 0, 2, 6, 12 and 24Â h. Headings of the selected clusters (1-16) utilized in the study are highlighted with blue color, while headings of the other clusters (A-Z) are highlighted in gray color. (XLSX 286 kb)
DOI: 10.5281/zenodo.14062243
title: Original data for "Charge-density-wave control by adatom manipulation and its effect on magnetic nanostructures"

description: We provide all original experimental data to the paper "Charge-density-wave control by adatom manipulation and its effect on magnetic nanostructures".
DOI: 10.5281/zenodo.14062244
title: Original data for "Charge-density-wave control by adatom manipulation and its effect on magnetic nanostructures"

description: We provide all original experimental data to the paper "Charge-density-wave control by adatom manipulation and its effect on magnetic nanostructures".
DOI: 10.6084/m9.figshare.c.3600809_d8.v1
title: Additional file 7: of Phylogenetic approaches to microbial community classification

description: Taxonomic composition of samples. The relative abundance of each group in subgingival and supragingival plaque is shown. Taxonomy is displayed from kingdom to species level. (XLSX 492 kb)
DOI: 10.6084/m9.figshare.c.3600809_d9.v1
title: Additional file 5: of Phylogenetic approaches to microbial community classification

description: OTU counts raw dataset. (TXT 8,494 kb)
DOI: 10.6084/m9.figshare.c.3600764_d11.v1
title: Additional file 18: Table E13. of Meta-analysis derived atopic dermatitis (MADAD) transcriptome defines a robust AD signature highlighting the involvement of atherosclerosis and lipid metabolism pathways

description: MTGDR results. (XLSX 9Â kb)
DOI: 10.6084/m9.figshare.c.3600809_d10.v1
title: Additional file 2: of Phylogenetic approaches to microbial community classification

description: Summary of microbiome samples. Human oral cavity samples came from HMP with associated abbreviations. OTUs were picked using a closed-reference strategy with a 97Â % identity threshold. (XLSX 32 kb)
DOI: 10.6084/m9.figshare.c.3600809_d11.v1
title: Additional file 8: of Phylogenetic approaches to microbial community classification

description: Functional raw dataset. (TXT 12,193 kb)
DOI: 10.6084/m9.figshare.c.3600845_d6.v1
title: Additional file 3: of MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics

description: List of restriction enzymes (mandatory input for COBRA-PCR and MSRE-PCR) in a text file one enzyme per line. (TXT 41 bytes)
DOI: 10.6084/m9.figshare.c.3600866_d1.v1
title: Additional file 2: of Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements

description: This sheet includes information about annotation, presence/absence polymorphisms and dN/dS for each of the gene models. (XLSX 12390Â kb)
DOI: 10.15468/dl.sx8xc8
title: Occurrence Download

description: A dataset listing the 8299 species recorded in GBIF matching the query:
{
 "DatasetKey" : [
 "is INPN - Données flore des CBN agrégées par la FCBN"
 ]
}

 The dataset's 8299 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0037513-241126133413365/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.3600884_d1.v1
title: Additional file 1: of Haemosporidian parasite prevalence, parasitemia, and diversity in three resident bird species at a shrubland dominated landscape of the Mexican highland plateau

description: GenBank accession numbers. Sequences 1 to 10 correspond to reference sequences in the NJ cladogram, 11 to 27 correspond to sequences obtained from samples of the canyon towhee (M. fusca) and 28 to 72 are sequences obtained from samples of the house finch (H. mexicanus). Sequences in bold are shown in the NJ cladogram. (CSV 4 kb)
DOI: 10.6084/m9.figshare.c.3600899_d7.v1
title: Additional file 3: Table S3. of Differential expression of conserved and novel microRNAs during tail regeneration in the lizard Anolis carolinensis

description: DESeq differential expression testing of microRNA between the regenerating green anole tail tip and base. (XLSX 85Â kb)
DOI: 10.6084/m9.figshare.c.3600899_d8.v1
title: Additional file 4: Table S4. of Differential expression of conserved and novel microRNAs during tail regeneration in the lizard Anolis carolinensis

description: List of microRNA targets predicted by both RNAhybrid and miRanda. (XLSX 2990Â kb)
DOI: 10.6084/m9.figshare.c.3600917_d1.v1
title: Additional file 2: of iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

description: Pentamer Z-scores. (XLSX 75 kb)
DOI: 10.6084/m9.figshare.c.3600899_d9.v1
title: Additional file 5: Table S5. of Differential expression of conserved and novel microRNAs during tail regeneration in the lizard Anolis carolinensis

description: Expression summary of down- or upregulated microRNAs and their mRNA targets. (XLSX 218Â kb)
DOI: 10.6084/m9.figshare.c.3600926_d1.v1
title: Additional file 4: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study

description: AF TableÂ 3: detailed medical history. Detailed medical history of each patient focussed on medical conditions at risk of cramps. (CSV 9Â kb)
DOI: 10.6084/m9.figshare.c.3600899_d10.v1
title: Additional file 2: Table S2. of Differential expression of conserved and novel microRNAs during tail regeneration in the lizard Anolis carolinensis

description: MicroRNA expression in green anole tail regeneration: counts from miRDeep2 and normalized DESeq values. (XLSX 120Â kb)
DOI: 10.6084/m9.figshare.c.3600926_d2.v1
title: Additional file 2: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study

description: AF TableÂ 1: detailed prevalence of cramps in the study population. Detailed presence of cramps, cramps related with sleep disturbance, cramps more frequent than 3 times a month, gender and age-group among the study population. (CSV 8Â kb)
DOI: 10.6084/m9.figshare.c.3600917_d4.v1
title: Additional file 3: of iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

description: iCLIP RNA targets with at least five SAFB1 tags. (XLSX 363 kb)
DOI: 10.6084/m9.figshare.c.3600926_d3.v1
title: Additional file 5: of Prevalence of cramps in patients over the age of 60 in primary care : a cross sectional study

description: AF TableÂ 4: detailed treatment. Detailed treatment of each patient, reporting also phytotherapy and homeopathy, without targeting medication at risk of cramps. (CSV 27Â kb)
DOI: 10.6084/m9.figshare.c.3600932_d3.v1
title: Additional file 5: of Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes

description: Genetic map markers defining the QTL region and corresponding physical map contigs. (XLSX 40 kb)
DOI: 10.5523/bris.1zjrkhdd6cstr2hj6yn4it9jze
title: Rapid and Sensitive Chemical Analysis of Individual Picolitre Droplets by Mass Spectrometry

description: Aerosol droplets are unique microcompartments containing microscopic amounts of material and exhibiting surprising chemical reactivity. Although a diverse set of tools exists to characterise the chemical composition of individual submicron particles in air, comparatively fewer approaches can chemically analyse individual, airborne picolitre droplets. We describe a novel approach for mass spectrometric analysis of individual aqueous picolitre droplets (~2-180 pL volume) containing down to ~1 pg analyte mass per droplet. Individual droplets are generated using a microdroplet dispenser, imparted a small amount of net charge, and guided to the inlet of a high-resolution mass spectrometer using a linear quadrupole-electrodynamic balance. Analyte molecules within the aqueous droplet are ionised using droplet assisted ionisation, where droplet breakup within the mass spectrometer inlet leads to generation of molecular ions. This single droplet mass spectrometry approach is demonstrated for small molecules and proteins. The approach generates clean mass spectra, permits timing of droplet delivery for chemical analysis, and, by avoiding a separate ionisation stage, avoids potential artefacts arising from current electrospray-based approaches for picolitre droplet analysis. It is anticipated this approach will permit exploration of the factors governing accelerated chemical reactions in aerosol droplets and will be suitable for sensitive analysis of particularly precious samples in different application domains.
DOI: 10.6084/m9.figshare.c.3600992_d1.v1
title: Additional file 2 of Characterizing exons and introns by regularity of nucleotide strings

description: MATLAB function for producing plots of the cumulative evolutionary slope with plotted averages for coding, noncoding, and combination regions. (M 3.94 kb)
DOI: 10.6084/m9.figshare.c.3600953_d9.v1
title: MOESM8 of Haematocrit, eggshell colouration and sexual signaling in the European starling (Sturnus vulgaris)

description: Additional file 8: Table S8. Raw data-individual eggs.
DOI: 10.6084/m9.figshare.c.3600992_d2.v1
title: Additional file 1 of Characterizing exons and introns by regularity of nucleotide strings

description: MATLAB function for producing the cumulative evolutionary slope for a DNA sequence. (M 1.44 kb)
DOI: 10.6084/m9.figshare.c.3600989_d2.v1
title: Additional file 2 of Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information

description: Sequence data. This archive contains data files of gap-free alignments of the ChIP-seq positive regions for each of the transcription factors CTCF, GABP, NRSF, SRF, and STAT1 in FASTA format. (ZIP 645 kb)
DOI: 10.6084/m9.figshare.c.3600953_d10.v1
title: MOESM9 of Haematocrit, eggshell colouration and sexual signaling in the European starling (Sturnus vulgaris)

description: Additional file 9: Table S9. Raw data-individual chicks.
DOI: 10.6084/m9.figshare.c.3601028_d1.v1
title: Additional file 5: Table S10. of Cyclic AMP signaling restricts activation and promotes maturation and antioxidant defenses in astrocytes

description: Antibodies used in this study. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3601028_d2.v1
title: Additional file 3: Tables S2–S8. of Cyclic AMP signaling restricts activation and promotes maturation and antioxidant defenses in astrocytes

description: Lists of genes regulated in cAMP-treated cells and present in published astrocyte signatures. Genes that are regulated in cAMP-treated cells (genes within the “core enrichment” as defined by GSEA analysis), and that are reported to be regulated in previously published astrocyte signatures: developing (Table S2), mature (Table S3), cytokine-treated (Table S4), LPS (Table S5), MCAO (Table S6), in vivo (Table S7) and in vitro (Table S8) astrocytes. The lists represent the respective intersections in the Venn diagrams of Figure 4C. In GSEA analysis, genes were ranked on the basis of signal-to-noise ratio within the microarray data, starting with strongly upregulated and ending with strongly downregulated genes. The third column of the tables indicate the rank of the respective gene, i.e. low rank values indicate strong upregulation and high ones close to the maximal value of 21,492 indicate strong downregulation. (XLS 108 kb)
DOI: 10.6084/m9.figshare.c.3601016_d4.v1
title: Additional file 5:Â Table S4. of VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

description: Two vcf files produced from the exome sequencing of the Capillary Leak Syndrome clinical case described in the results section, consisting of the inflicted child as well as cousin. (GZ 13018Â kb)
DOI: 10.6084/m9.figshare.c.3601022_d4.v1
title: Additional file 1 of Do little interactions get lost in dark random forests?

description: Software package. Version of the software package ranger, including the pairwise permutation importance measure. (GZ 39.9 kb)
DOI: 10.6084/m9.figshare.c.3601019_d5.v1
title: Additional file 9: Table S7. of The genome of the emerging barley pathogen Ramularia collo-cygni

description: RT-PCR analysis of Ramularia collo-cygni homologs of dothistromin biosynthesis genes and predicted secondary metabolism genes on Contig17. (XLSX 13 kb)
DOI: 10.6084/m9.figshare.c.3601019_d6.v1
title: Additional file 12: Table S9. of The genome of the emerging barley pathogen Ramularia collo-cygni

description: Details of fungal genomes used for comparative genomics in this study. (XLSX 17 kb)
DOI: 10.6084/m9.figshare.c.3601016_d5.v1
title: Additional file 3: Table S2. of VarElect: the phenotype-based variation prioritizer of the GeneCards Suite

description: Gene lists and corresponding phenotypes for Phenomyzer and Exomiser benchmarking. (XLSX 16.0 kb)
DOI: 10.6084/m9.figshare.c.3601028_d4.v1
title: Additional file 1: Table S1. of Cyclic AMP signaling restricts activation and promotes maturation and antioxidant defenses in astrocytes

description: Full list of significantly regulated genes in cAMP-treated cells. Differential expression analysis on a gene-by-gene basis was done using linear models (limma). The table contains all genes with FDR q-values &lt;5 % and absolute fold changes &gt; 1.2 and is sorted on the basis of fold changes in decreasing order. The first eight columns show a color representation of the log2ratios for each two-color hybridization of a cAMP-treated together with a control sample. The sign of dye-swap hybridization log2ratios (indicated by ‘DS’ in the column name) was flipped, such that values have the same “direction” as in the direct hybridizations, i.e. red (green) indicates up- (down-) regulation in cAMP-treated as compared to Control. The 9th column is the average log2ratio between cAMP-treated and Control samples. In addition to gene symbol and gene description, the remaining three columns show (symmetric) fold changes, limma p-values and FDR q-values. (XLS 4198 kb)
DOI: 10.6084/m9.figshare.c.3601040_d1.v1
title: Additional file 10: Table S8 of A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses

description: shows the functional enrichment analysis of p50/RelA and p52/RelB targets using ‘Gene Ontology (GO) for biological processes’ analyses. (XLSX 6646 kb)