cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3617339_d4.v1
title: Additional file 5: Figure S1. of Transcriptional cellular responses in midgut tissue of Aedes aegypti larvae following intoxication with Cry11Aa toxin from Bacillus thuringiensis

description: RNAseq and log2 transformed RT-qPCR fold changes. Data is presented for RNAseq and RT-qPCR at 3, 6, 9, and 12 h of an LC50 Cry11Aa treatment. Also shown are RT-qPCR values for 9 and 12 h of unexposed larvae or Cry11Aa non-toxic mutants treatments. All log2 fold changes are referred to control larvae at the start of respective treatment. Panel A and B show genes with high correlation between RNAseq data and RT-qPCR of Cry11Aa. Panel C shows the three genes with low or no positive correlation between these data. (ZIP 779 kb)
DOI: 10.6084/m9.figshare.c.3617363_d1.v1
title: Additional file 9: of Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus

description: SNVs of ASGV isolate Cuiguan in ASGV-infected sample. (XLSX 13Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d7.v1
title: Additional file 6: Table S10. of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Putative proteases predicted by the batch Blast against the MEROPS database. (XLSX 53Â kb)
DOI: 10.6084/m9.figshare.c.3619241_d8.v1
title: Additional file 4: Table S4. of Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

description: Putative secreted proteins involved in PHI, CAZy, Protease, and CYP450. (XLSX 134Â kb)
DOI: 10.6084/m9.figshare.c.3619256_d2.v1
title: Additional file 2: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

description: A table listing the gene ontology terms of differentially expressed genes between MCF-10A and MCF-7 cells. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.c.3619256_d3.v1
title: Additional file 3: of Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells

description: A table listing the gene ontology terms of the MCF-7 up-regulated genes that are on small chromosomes and are on compartment switch regions. (XLSX 5 kb)
DOI: 10.6084/m9.figshare.c.3619268_d2.v1
title: Additional file 2: of Novel genetic risk variants for pediatric celiac disease

description: Regulome DB questioned a possible role of the variants of interest in terms of transcription factor binding sites, chromatin states, eQTLs, differentially methylated regions, validated functional SNPs and DNase sensitivity. All variants had minimum or no impact. (XLSX 3.62 mb)
DOI: 10.6084/m9.figshare.c.3619274_d1.v1
title: MOESM2 of Microsatellite loci for Urochloa decumbens (Stapf) R.D. Webster and cross-amplification in other Urochloa species

description: Additional file 2. Magnitude of ΔK determined in STRUCTURE analysis of K, calculated following the ΔK method proposed by Evanno et al. [24].The highest ΔK value corresponds to the optimal K.
DOI: 10.5281/zenodo.14060443
title: Designing Quinazoline Derivatives to Prevent Alzheimer's disease in silico and in vitro studies

description: Input files, parameter files, topology files for molecular docking, MD, and perturbation simulations
DOI: 10.5281/zenodo.14060444
title: Designing Quinazoline Derivatives to Prevent Alzheimer's disease in silico and in vitro studies

description: Input files, parameter files, topology files for molecular docking, MD, and perturbation simulations
DOI: 10.5281/zenodo.14512122
title: Designing Quinazoline Derivatives to Prevent Alzheimer's disease in silico and in vitro studies

description: Input files, parameter files, topology files for molecular docking, MD, and perturbation simulations
DOI: 10.6084/m9.figshare.c.3619274_d2.v1
title: MOESM3 of Microsatellite loci for Urochloa decumbens (Stapf) R.D. Webster and cross-amplification in other Urochloa species

description: Additional file 3. Jaccard’s coefficient for 34 genotypes of Urochloa spp. evaluated using 82 microsatellite markers. Individuals are identified according to their EBC codes (Table 1).
DOI: 10.6084/m9.figshare.c.3621095_d8.v1
title: Additional file 3: of The trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by Pichia pastoris

description: Extracellular flux parameters data for GSLAC clone. XLS 38 kb)
DOI: 10.6084/m9.figshare.c.3621095_d9.v1
title: Additional file 5: of The trade-off of availability and growth inhibition through copper for the production of copper-dependent enzymes by Pichia pastoris

description: Flux ratios and mass distribution vectors of amino acids. (XLS 192 kb)
DOI: 10.6084/m9.figshare.c.3621155_d1.v1
title: Additional file 2: of Innate immunity based cancer immunotherapy: B16-F10 murine melanoma model

description: Fig5_DATA. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.c.3621155_d2.v1
title: Additional file 1: of Innate immunity based cancer immunotherapy: B16-F10 murine melanoma model

description: Fig1-4,6,7_DATA. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.c.3621137_d10.v1
title: Additional file 3:Â Dataset 1. of A critical role for the Drosophila dopamine D1-like receptor Dop1R2 at the onset of metamorphosis

description: Summary of microarray data. (XLSX 61 kb)
DOI: 10.6084/m9.figshare.c.3621167_d1.v1
title: Additional file 4: of Gene expression profiling of trout regenerating muscle reveals common transcriptional signatures with hyperplastic growth zones of the post-embryonic myotome

description: Major functional categories of cluster III and lists of genes that formed them. (XLSX 62 kb)
DOI: 10.6084/m9.figshare.c.3623258_d7.v1
title: MOESM8 of A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data

description: Additional file 8. Average abundance (%) of the 10 most abundant Clostridiales genera in the 401 MetaHit samples analyzed in this work. The first column indicates the putative presence (+) or absence (−) of a CopZ homolog as determined through independent BLASTP searches using B. subtilis and S. aureus CopZ protein sequences with a cutoff e-value of 10−15. Table compiled from data reported in Li et al. Nature Biotechnology 32, 834–841 (2014).
DOI: 10.6084/m9.figshare.c.3623282_d1.v1
title: Additional file 1: of Cutaneous stimulation at the ankle: a differential effect on proprioceptive postural control according to the participants’ preferred sensory strategy

description: Data sets of the study. (XLSX 53 kb)
DOI: 10.6084/m9.figshare.c.3623258_d8.v1
title: MOESM7 of A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data

description: Additional file 7. Posterior probability assigned to eggNOG/COG identifiers after sensitivity adjustment with θ = 6.65. The table lists the eggNOG/COG identifier, its eggNOG 4.0 annotation and functional category, the number of mapped promoters before and after sensitivity adjustment and the posterior probability for all eggNOG/COGs with at least 5 promoters mapping to them after sensitivity adjustment.
DOI: 10.6084/m9.figshare.c.3623294_d2.v1
title: Additional file 3: of Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms

description: Biological evidence. In this file, the IPN nodes, the MCL modules, the human proteins in OPSs and the enriched terms of proteins consist IPN modules are presented. The enrichment analysis of each module presented separately in different sheets. The human proteins were used to perform this analysis. (XLSX 38Â kb)
DOI: 10.6084/m9.figshare.c.3623309_d1.v1
title: Additional file 3 of Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

description: Code for DNase-seq data. Software for our method for DNase-seq data in the form of an R script. (ZIP 2 kb)
DOI: 10.6084/m9.figshare.c.3623309_d2.v1
title: Additional file 2 of Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data

description: TCGA A/B compartments. Estimated compartments for 12 TCGA cancers using 450 k methylation data, as a concatenated TXT file. There are six columns; the file is tab separated and has a header. Column 1 (tcga_code) is the TCGA short code for the cancer. Columns 2 (chr), 3 (start) and 4 (end) are the chromosomal coordinates of each region, in hg19 coordinates (1-based) and at 100-kb resolution. Column 5 (eigen) is the estimated first eigenvector. Column 6 (domain) is whether or not the region is estimated to be in open or closed chromatin. (TXT 13619 kb)
DOI: 10.15468/dl.pygrk8
title: Occurrence Download

description: A dataset containing 4312 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is iNaturalist Research-grade Observations",
 "OccurrenceStatus is Present",
 "StateProvince is one of (MAryland, Maryland, Maryland (State), Maryland (MD))",
 "TaxonKey is Pentatomidae"
 ]
}

 The dataset includes 4312 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038617-241126133413365/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.3625340_d1.v1
title: Additional file 7: Table S6. of Phytohormone balance and stress-related cellular responses are involved in the transition from bud to shoot growth in leafy spurge

description: Differentially-expressed sugar transporter genes. (XLSX 18Â kb)
DOI: 10.6084/m9.figshare.c.3625340_d2.v1
title: Additional file 6: Table S5. of Phytohormone balance and stress-related cellular responses are involved in the transition from bud to shoot growth in leafy spurge

description: Central hubs for expression targets and small molecules based on SNEA. (XLSX 24Â kb)
DOI: 10.6084/m9.figshare.c.3625343_d2.v1
title: MOESM3 of 
                     Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass

description: Additional file 3. Complete protein reports of Penicillium echinulatum strains in each condition. This table shows important data of proteomic analysis: number of peptides used for the identification and sequence coverage (%).
DOI: 10.6084/m9.figshare.c.3625355_d1.v1
title: MOESM1 of Analysis of Axin2 expression and function in murine models for pancreatic cancer

description: Additional file 1. In the Supplemental Material Section results from beta-galactosidase stainings, blood glucose concentrations, body weights, tumor weights, as well as number of leucocytes, lymphocytes and monocytes plus ganulocytes are presented.
DOI: 10.6084/m9.figshare.c.3625358_d1.v1
title: Additional file 1: Table S1. of Predicting multi-class responses to preoperative chemoradiotherapy in rectal cancer patients

description: Clinical information. (XLSX 19.5 kb)
DOI: 10.6084/m9.figshare.c.3625340_d3.v1
title: Additional file 5: Table S4. of Phytohormone balance and stress-related cellular responses are involved in the transition from bud to shoot growth in leafy spurge

description: AraCyc pathways that are over-represented for comparisons 6 h vs. 0 h, 24 h vs. 0 h, and 72 h vs. 0 h based on GSEA. (XLSX 91 kb)
DOI: 10.6084/m9.figshare.c.3625340_d4.v1
title: Additional file 3: Table S2. of Phytohormone balance and stress-related cellular responses are involved in the transition from bud to shoot growth in leafy spurge

description: Heat map diagram showing changes in transcript abundance obtained by RNA-seq vs. RT-qPCR analysis. (XLSX 37Â kb)
DOI: 10.6084/m9.figshare.c.3625343_d3.v1
title: MOESM2 of 
                     Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass

description: Additional file 2. Comparative analysis of the most expressed proteins in each condition for each Penicillium echinulatum strain. This comparative analysis was based on the list, in order, of ten proteins with more spectra found in each carbon source in the wild type 2HH and mutant S1M29 and also the most expressed proteins when analyzing both strains.
DOI: 10.6084/m9.figshare.c.3626300_d1.v1
title: Additional file 4: of SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs

description: Prodigal annotation of the C. coli BFR-CA-9557. Annotation of the C. coli BFR-CA-9557 genome using the Prodigal/Prokka annotation pipeline. (XLS 727 kb)
DOI: 10.6084/m9.figshare.c.3626282_d9.v1
title: Additional file 4: of The parameter sensitivity of random forests

description: Pairwise t-test results for n tree intra-parameter groups for the low p/n data. All p-values were adjusted using a Benjamini-Hochberg procedure. The only n tree value found to differ from every other n tree group was 10. (TXT 456 bytes)
DOI: 10.6084/m9.figshare.c.3626282_d10.v1
title: Additional file 8: of The parameter sensitivity of random forests

description: AUC results for high p/n data. Validation results for all high p/n models (n = 1000) using the MSKCC data, DFCI data, and combined MSKCC and DFCI data. The AUC results and ranks are provided for each combination of n tree , m try and sampsize parameters. Lower ranks represent higher model performance with 1 representing the most accurate model and 1000 representing the worst performing model. Logical columns are present to indicate whether a parameter set performed better than the default or well across all validation sets. Model performance was defined as good if the parameter set resulted in an AUC of &gt; 0.6 across all validation sets. The default settings (n tree  = 500, m try  = 110, sampsize = 255) are found on row 596 of the table. (CSV 28 kb)
DOI: 10.6084/m9.figshare.c.3626300_d2.v1
title: Additional file 3: of SMRT sequencing of the Campylobacter coli BfR-CA-9557 genome sequence reveals unique methylation motifs

description: RAST annotation of the C. coli BFR-CA-9557. Annotation of the C. coli BFR-CA-9557 genome using the rapid annotation using subsystem technology platform (RAST, http://rast.nmpdr.org ). (XLS 3605 kb)
DOI: 10.6084/m9.figshare.c.3626312_d1.v1
title: Additional file 1: Table S1. of A new polymorphism on chromosome 6 associated with bolting tendency in sugar beet

description: Information on 192 SNPs used in the study. (XLSX 37Â kb)
DOI: 10.6084/m9.figshare.c.3626282_d12.v1
title: Additional file 17: of The parameter sensitivity of random forests

description: Parameter grid for predicting performance. A summary table of parameters that were used to perform model tuning for predicting AUC using a subset of parameters, n tree , m try and sampsize. A total of 162 parameters were used in model tuning and the optimal parameters (n tree  = 200, m try  = 2, sampsize = 200) were selected to fit the final model. (CSV 124 bytes)
DOI: 10.6084/m9.figshare.c.3626279_d8.v1
title: Additional file 7: Table S4. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

description: A list of differentially expressed intergenic and antisense-strand regions. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3626282_d13.v1
title: Additional file 6: of The parameter sensitivity of random forests

description: Pairwise t-test results for m try intra-parameter groups for the low p/n data. All p-values were adjusted using a Benjamini-Hochberg procedure. Each sampsize group was found to differ from at least 12 other groups. (TXT 2 kb)
DOI: 10.6084/m9.figshare.c.3626279_d9.v1
title: Additional file 2: Table S1. of Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture

description: A complete list of genes that are differentially expressed in response to nitrogen limitation in M. smegmatis. (XLSX 2413Â kb)
DOI: 10.6084/m9.figshare.c.3626282_d14.v1
title: Additional file 11: of The parameter sensitivity of random forests

description: Pairwise t-test results for m try intra-parameter groups for the combined NSCLC validation data. All p-values were adjusted using a Benjamini-Hochberg procedure. In general lower m try values were found to differ significantly from higher m try values for example, m try 1 from m try 110â  â  â  2200. (TXT 1009 bytes)
DOI: 10.6084/m9.figshare.c.3627371_d1.v1
title: Additional file 2: of The common redstart as a suitable model to study cuckoo-host coevolution in a unique ecological context

description: Raw dataset used in this study. (XLSX 43 kb)
DOI: 10.6084/m9.figshare.c.3627374_d2.v1
title: Additional file 2: of Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

description: The calculated lengths (nt) of all the mRNA-coding nuclear transcripts (GRCh37) along with the number of exons, introns and their length fractions. The file is in the comma-separated CSV format. (CSV 2851 kb)
DOI: 10.6084/m9.figshare.c.3627374_d3.v1
title: Additional file 3: of Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

description: All the KEGG pathway and GO term analyses data used in this work. KEGG pathways and GO terms significantly enriched in the top genes by the transcript length, top genes by summed exon length, genes with greater than 3 transcript variants, and KEGG pathways significantly enriched in ASD-associated genes are presented. The data include the full list of the hit gene names. The file is in the Excel XLSX format. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.c.3628406_d2.v1
title: Additional file 6: of Detailed phenotyping identifies genes with pleiotropic effects on body composition

description: The signed t-values of SNP effects (300,001 to 450,000 in â  chromosome: positionâ   order) for the 56 traits used in multi-trait, meta-analysis. (GZ 30638Â kb)
DOI: 10.6084/m9.figshare.c.3628397_d6.v1
title: Additional file 5: of A transposable element insertion in the susceptibility gene CsaMLO8 results in hypocotyl resistance to powdery mildew in cucumber

description: Complete overview of putative LTRs and putative TEs homologous to the TE identified in CsaMLO8. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.c.3628415_d1.v1
title: Additional file 2: Figure S2. of An 8-gene mRNA expression profile in circulating tumor cells predicts response to aromatase inhibitors in metastatic breast cancer patients

description: Kaplan-Meier curve as defined by CTC count for the total cohort of 78 patients. Blue (0): &lt;5 CTCs at baseline; red (1): â Ľ5 CTCs at baseline. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3628406_d4.v1
title: Additional file 4: of Detailed phenotyping identifies genes with pleiotropic effects on body composition

description: The signed t-values of SNP effects (1 to 150,000 in â  chromosome: positionâ   order) for the 56 traits used in multi-trait, meta-analysis. (GZ 30545Â kb)
DOI: 10.6084/m9.figshare.c.3628406_d5.v1
title: Additional file 3: Table S1. of Detailed phenotyping identifies genes with pleiotropic effects on body composition

description: A list of the overlapped candidate genes in QTL regions from our sheep study with genes associated with body mass index and height in human. (XLSX 15Â kb)
DOI: 10.6084/m9.figshare.c.3629417_d5.v1
title: Additional file 3: Table S2. of Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

description: InterPro functional domains associated with the proteomes and secretomes of fungal genomes used in this study. (XLSX 645 kb)
DOI: 10.6084/m9.figshare.c.3629417_d6.v1
title: Additional file 6: Table S4. of Gene family expansions and contractions are associated with host range in plant pathogens of the genus Colletotrichum

description: Numbers of extracellular secreted protease homologs classified according to the MEROPS database 10.0 [45] in Colletotrichum and other fungal genomes used in this study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.c.3629483_d1.v1
title: Additional file 1: of Neuro-musculoskeletal simulation of instrumented contracture and spasticity assessment in children with cerebral palsy

description: Individual subject data. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.c.3629489_d1.v1
title: Additional file 2: of Naive Bayes classifiers for verbal autopsies: comparison to physician-based classification for 21,000 child and adult deaths

description: R code used to produce the results in this study.(ZIP 101 kb)
DOI: 10.6084/m9.figshare.c.3630449_d3.v1
title: Additional file 2 of Does conservation account for splicing patterns?

description: Upstream and downstream ISSs and ISEs. (CSV 1 kb)
DOI: 10.6084/m9.figshare.c.3630461_d3.v1
title: Additional file 2: of Dispersal variability and associated population-level consequences in tree-killing bark beetles

description: Model version used for this study (IPS 1.1). (NLOGO 31 kb)
DOI: 10.6084/m9.figshare.c.3631382_d1.v1
title: Additional file 1: Table S1. of The expression of microRNA 574-3p as a predictor of postoperative outcome in patients with esophageal squamous cell carcinoma

description: The relationship between the expression of the 20 miRNAs in the tumors (T/N ratio) and clinicopathological features of the patients. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3631388_d1.v1
title: Additional file 1: Table S1. of Influences on teleconsultation project utilization rates: the role of dominant logic

description: Teleconsultation projects background and demographics. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.c.3631397_d2.v1
title: Additional file 1: of An algorithm for the reduction of genome-scale metabolic network models to meaningful core models

description: Comparison of flux variabilities in ColiGS, ColiCore, and ColiPrunedComp for three different growth scenarios. (XLS 382 kb)
DOI: 10.6084/m9.figshare.c.3632339_d4.v1
title: MOESM2 of Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum

description: Additional file 2. Multiple alignment used for the phylogenetic analysis.
DOI: 10.6084/m9.figshare.c.3632327_d9.v1
title: Additional file 8: of Comparative genomics and prediction of conditionally dispensable sequences in legumeâ  infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

description: Repeat analysis. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3632324_d11.v1
title: Additional file 6: of Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick

description: Differential expression analysis results for all pairwise comparisons between ganglia using both DESeq (i) and EdgeR (ii). Data are available as compiled .xlsx spreadsheets (A) or individual .csv files (B). (ZIP 24942 kb)
DOI: 10.6084/m9.figshare.c.3632327_d10.v1
title: Additional file 13: of Comparative genomics and prediction of conditionally dispensable sequences in legumeâ  infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

description: Dispensable scaffold predictions in Fom -5190, Foc -38-1 and Fop -37622. (XLS 2255 kb)
DOI: 10.6084/m9.figshare.c.3632339_d6.v1
title: MOESM3 of Conservation and divergence of bHLH genes in the calcisponge Sycon ciliatum

description: Additional file 3. Matrix of gene expression levels calculated as sums of the posterior probability of each read coming from a given gene over all reads (expected_count metrics calculated with the RSEM package). First row: sample names, second row: replica names (reflecting names of the source RNASeq libraries), first column: gene identifiers.
DOI: 10.6084/m9.figshare.c.3632357_d1.v1
title: MOESM2 of Genetic diversity of Plasmodium falciparum in human malaria cases in Mali

description: Additional file 2. Microsatellite data of the genotyped samples. The allele length (in base pairs) for each Plasmodium falciparum tested loci (Poly α, TA109, TA1, TA81, TA42, ARA2, PfPK2, Pfg377) is provided. The empty cells of the Table correspond to negative loci.