cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3816340_d9.v1
title: Additional file 18: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Known upregulated transcription factors in T. reesei RUT-C30 transcriptome. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3816340_d9
title: Additional file 18: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Known upregulated transcription factors in T. reesei RUT-C30 transcriptome. (XLSX 19 kb)
DOI: 10.6084/m9.figshare.c.3816340_d10
title: Additional file 19: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Upregulated transcription factor-likes in both A. niger N402 and T. reesei RUT-C30 transcriptomes. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.c.3816340_d11.v1
title: Additional file 1: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Result of RNA sequencing for A. niger N402 and T. reesei RUT-C30 grown on sugarcane SEB and fructose. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.c.3816340_d22.v1
title: Additional file 9: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Validation of T. reesei RUT-C30 RNA-seq data by RT-qPCR. (XLSX 320 kb)
DOI: 10.6084/m9.figshare.c.3816340_d21
title: Additional file 8: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Validation of A. niger N402 RNA-seq data by RT-qPCR. (XLSX 355 kb)
DOI: 10.6084/m9.figshare.c.3816340_d21.v1
title: Additional file 8: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Validation of A. niger N402 RNA-seq data by RT-qPCR. (XLSX 355 kb)
DOI: 10.6084/m9.figshare.c.3816340_d22
title: Additional file 9: of Comparative transcriptome analysis reveals different strategies for degradation of steam-exploded sugarcane bagasse by Aspergillus niger and Trichoderma reesei

description: Validation of T. reesei RUT-C30 RNA-seq data by RT-qPCR. (XLSX 320 kb)
DOI: 10.15468/dl.5v7nj3
title: Occurrence Download

description: A dataset containing 347 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Paralvinella palmiformis Desbruyères & Laubier, 1986"
 ]
}

 The dataset includes 347 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038992-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.emvhph
title: Occurrence Download

description: A dataset containing 1194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Stachys heraclea All., Stachys phlomoides Willd., Stachys valentina Lag., Stachys barbigera Viv., Stachys betonicifolia Pers., Sideritis heraclea Colebr. ex Benth., Stachys heraclea subsp. malessana Degen & Hervier, Stachys barbata Lapeyr., Sideritis heraclea Colebr., Stachys heraclea var. barbigera (Viv.) Nyman)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 2000"
 ]
}

 The dataset includes 1194 records from 78 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038993-241126133413365/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.3816466_d2.v1
title: Additional file 2: of miRNome landscape analysis reveals a 30 miRNA core in retinoblastoma

description: Validation data and list of miRNA clusters from the Rb landscape. (XLSX 726 kb)
DOI: 10.6084/m9.figshare.c.3816466_d2
title: Additional file 2: of miRNome landscape analysis reveals a 30 miRNA core in retinoblastoma

description: Validation data and list of miRNA clusters from the Rb landscape. (XLSX 726 kb)
DOI: 10.6084/m9.figshare.c.3816451_d6.v1
title: Additional file 2: of Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

description: Segmentally and tandemly duplicated AcMYB gene pairs. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3816451_d6
title: Additional file 2: of Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

description: Segmentally and tandemly duplicated AcMYB gene pairs. (XLSX 12Â kb)
DOI: 10.6084/m9.figshare.c.3816466_d3.v1
title: Additional file 3: of miRNome landscape analysis reveals a 30 miRNA core in retinoblastoma

description: Analysis of target genes, pathways, cellular processes and miRNAs located in lost regions. (XLSX 148 kb)
DOI: 10.6084/m9.figshare.c.3817558_d1.v1
title: Additional file 1: of Genomic variability in Mexican chicken population using copy number variants

description: Sheet 1. List of CNVRs detected in this study; Sheet 2: comparison of the CNVR detected in this study with published ones; Sheet 3: annotation of CNVRs common among this and published studies; Sheet 4: annotated gene in CNVRs; sheet 5: Significant Go Term_Panther; sheet 6: QTLRs mapped within CNVRs (XLSX 501 kb).
DOI: 10.6084/m9.figshare.c.3817558_d1
title: Additional file 1: of Genomic variability in Mexican chicken population using copy number variants

description: Sheet 1. List of CNVRs detected in this study; Sheet 2: comparison of the CNVR detected in this study with published ones; Sheet 3: annotation of CNVRs common among this and published studies; Sheet 4: annotated gene in CNVRs; sheet 5: Significant Go Term_Panther; sheet 6: QTLRs mapped within CNVRs (XLSX 501 kb).
DOI: 10.15468/dl.466nmp
title: Occurrence Download

description: A dataset containing 191 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Urocampus nanus Günther, 1870"
 ]
}

 The dataset includes 191 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038994-241126133413365/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.3817633_d1.v1
title: Additional file 1: Table S1. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Test of means (t-test) of intramuscular fat (IMF), backfat thickness (BFT) and ribeye area (REA) between groups with High and Low REA and BFT in the Longissimus dorsi muscle of Nellore steers. (XLS 33Â kb)
DOI: 10.6084/m9.figshare.c.3817633_d1
title: Additional file 1: Table S1. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Test of means (t-test) of intramuscular fat (IMF), backfat thickness (BFT) and ribeye area (REA) between groups with High and Low REA and BFT in the Longissimus dorsi muscle of Nellore steers. (XLS 33Â kb)
DOI: 10.6084/m9.figshare.c.3817633_d2.v1
title: Additional file 2: Table S2. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Differentially expressed genes obtained between high and low genomic breeding value groups for ribeye area in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 45Â kb)
DOI: 10.6084/m9.figshare.c.3817633_d2
title: Additional file 2: Table S2. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Differentially expressed genes obtained between high and low genomic breeding value groups for ribeye area in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 45Â kb)
DOI: 10.6084/m9.figshare.c.3817633_d3.v1
title: Additional file 3: Table S3. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Differentially expressed genes obtained between high and low genomic breeding value groups for backfat thickness in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.c.3817633_d3
title: Additional file 3: Table S3. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Differentially expressed genes obtained between high and low genomic breeding value groups for backfat thickness in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 31Â kb)
DOI: 10.6084/m9.figshare.c.3817633_d4.v1
title: Additional file 4: Table S4. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

description: Functional enrichment analysis performed by DAVID (p value &lt;0.1) comparing high and low genomic breeding value groups for backfat thickness. The table contains Gene Ontology category, identification and description, p value, p value adjusted for a false discovery rate of 10% and the DE genes for each category. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.c.3817654_d3.v1
title: MOESM5 of From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures

description: Additional file 3: Table S5. Differentially expressed proteins.
DOI: 10.6084/m9.figshare.c.3817654_d3
title: MOESM5 of From grass to gas: microbiome dynamics of grass biomass acidification under mesophilic and thermophilic temperatures

description: Additional file 3: Table S5. Differentially expressed proteins.
DOI: 10.6084/m9.figshare.c.3817738_d3.v1
title: MOESM3 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

description: Additional file 3: Table S1. Prediction accuracy and bias for BayesA haplotype models.
DOI: 10.6084/m9.figshare.c.3817738_d4.v1
title: MOESM4 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

description: Additional file 4: Table S2. Mean square errors for the BayesA models.
DOI: 10.6084/m9.figshare.c.3817738_d5.v1
title: MOESM5 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

description: Additional file 5: Table S3. Accuracy of BayesN model with Π = 0.5 fitting two or all SNPs per window.
DOI: 10.6084/m9.figshare.c.3817738_d3
title: MOESM3 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

description: Additional file 3: Table S1. Prediction accuracy and bias for BayesA haplotype models.
DOI: 10.6084/m9.figshare.c.3817738_d4
title: MOESM4 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

description: Additional file 4: Table S2. Mean square errors for the BayesA models.
DOI: 10.6084/m9.figshare.c.3817738_d5
title: MOESM5 of Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population

description: Additional file 5: Table S3. Accuracy of BayesN model with Π = 0.5 fitting two or all SNPs per window.
DOI: 10.5281/zenodo.13841240
title: The Data for Cloud Removal in Full-disk Solar Images Using Deep Learning

description: Cloud Removal in Full-disk Solar Images Using Deep Learning. For more information, please refer to README.md.

Please note that the data and model parameters zip is not available in github. Please download them in this file.

If you need help, feel free to contact me at szh@kust.edu.cn or dp24163@163.com.
DOI: 10.6084/m9.figshare.c.3817975_d3.v1
title: Additional file 3: Table S2. of Prevalence, incidence and carrier frequency of 5q–linked spinal muscular atrophy – a literature review

description: Copy numbers SMN1 gene in general population. (XLS 52 kb)
DOI: 10.6084/m9.figshare.c.3817975_d3
title: Additional file 3: Table S2. of Prevalence, incidence and carrier frequency of 5q–linked spinal muscular atrophy – a literature review

description: Copy numbers SMN1 gene in general population. (XLS 52 kb)
DOI: 10.6084/m9.figshare.c.3818002_d1.v1
title: Additional file 1 of sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

description: ecolisim_script.R, example R script to simulate expression profiles and the inference of network from the simulated profiles using BC3NET. (R 2 kb)
DOI: 10.6084/m9.figshare.c.3818002_d1
title: Additional file 1 of sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

description: ecolisim_script.R, example R script to simulate expression profiles and the inference of network from the simulated profiles using BC3NET. (R 2 kb)
DOI: 10.6084/m9.figshare.c.3818020_d1.v1
title: Additional file 1: of Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature

description: Genes significantly differentially expressed between lcSSc and control groups. Green cells: genes with increased expression in controls. Yellow cells: genes with increased expression in lcSSc samples. (XLSX 16 kb)
DOI: 10.5284/1124552
title: Images from a Level 2 Archaeological Bulding Recording Survey at Former Ropery at Argyle Street, Hebburn, Tyne and Wear, September 2023

description: This collection comprises images from a level 2 archaeological bulding recording survey at former ropery at Argyle Street, Hebburn, Tyne and Wear, undertaken by Archaeological Services Durham University in September 2023.
DOI: 10.6084/m9.figshare.c.3818020_d4.v1
title: Additional file 4: of Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature

description: g:Profiler output for 70 genes with increased expression in the limited-1 group annotated to cardiovascular system development. Additional file 4 contains the following column headers. Descriptions are as follows: p value: significance of enrichment in a given term corrected for multiple hypothesis testing using default g:GOSt method g:SCS. Q&T: overlap between genes in the query (Q) and genes in the genome annotated to a given term (T). t type: term category - Gene Ontology: Biological Process (BP), Molecular Function (MF), Cellular Component (CC); KEGG (keg); Reactome (rea). t name: term name. Q&T list: list of genes forming the overlap between query (Q) and genome lists for a given term (T). (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3818020_d4
title: Additional file 4: of Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature

description: g:Profiler output for 70 genes with increased expression in the limited-1 group annotated to cardiovascular system development. Additional file 4 contains the following column headers. Descriptions are as follows: p value: significance of enrichment in a given term corrected for multiple hypothesis testing using default g:GOSt method g:SCS. Q&T: overlap between genes in the query (Q) and genes in the genome annotated to a given term (T). t type: term category - Gene Ontology: Biological Process (BP), Molecular Function (MF), Cellular Component (CC); KEGG (keg); Reactome (rea). t name: term name. Q&T list: list of genes forming the overlap between query (Q) and genome lists for a given term (T). (XLSX 29 kb)
DOI: 10.6084/m9.figshare.c.3818047_d1.v1
title: Additional file 1: Table S1. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: List of Dipteran species analysed. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3818047_d1
title: Additional file 1: Table S1. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: List of Dipteran species analysed. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3818047_d2
title: Additional file 2: Table S2. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: List of viral genomes used for in silico screening of Dipteran genomes. The only DNA arbovirus is in yellow. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3818047_d2.v1
title: Additional file 2: Table S2. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: List of viral genomes used for in silico screening of Dipteran genomes. The only DNA arbovirus is in yellow. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3818059_d1
title: MOESM1 of The potential of shifting recombination hotspots to increase genetic gain in livestock breeding

description: Additional file 1: Table S1. Mean and variance of 10 replicates across all scenarios.This file presents the data used for plotting the mean and variance across each replicate for each scenario for the 80 generations of selection.
DOI: 10.6084/m9.figshare.c.3818047_d3.v1
title: Additional file 3: Table S3. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: Description of all identified NIRVS (XLSX 132 kb)
DOI: 10.6084/m9.figshare.c.3818041_d5
title: MOESM5 of 
                     Drosophila CP190- and dCTCF-mediated enhancer blocking is augmented by SUMOylation

description: Additional file 5: Table S3. Flag-SUMO and CP190 staining after luc or after Aos/Uba2 knock down. Analyses of CP190 intensity maxima as well as determination of FLAG-dSUMO signal intensity were performed with Fiji, the image processing package of ImageJ. FLAG-dSUMO signal intensity measured by integrated density was background-corrected.
DOI: 10.6084/m9.figshare.c.3818068_d2.v1
title: Additional file 2 of Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

description: Metabolites in iNS934. List of all metabolites in N. salina model iNS934. (XLSX 122 kb)
DOI: 10.6084/m9.figshare.c.3818047_d7.v1
title: Additional file 7: Table S6. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: (A) piRNA coverage at NIRVS loci. (B) NIRVS transcriptional activity. (XLSX 90 kb)
DOI: 10.6084/m9.figshare.c.3818068_d2
title: Additional file 2 of Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

description: Metabolites in iNS934. List of all metabolites in N. salina model iNS934. (XLSX 122 kb)
DOI: 10.60656/acf41e78ff794e46
title: Custom collection of ice water content data from Bucharest, Chilbolton, Galați, Hyytiälä, Jülich, and 7 other sites on 1 Feb 2023
DOI: 10.6084/m9.figshare.c.3818047_d7
title: Additional file 7: Table S6. of Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus

description: (A) piRNA coverage at NIRVS loci. (B) NIRVS transcriptional activity. (XLSX 90 kb)
DOI: 10.34636/dmportal/q5grto
title: Predictive Models for Rice Quality Traits Using MATLAB

description: The purpose of this dataset is to provide predictive models for assessing rice quality traits (e.g., amylose content, viscosity profiles) and classifying rice types using Near-Infrared (NIR) spectroscopy. These models were developed in MATLAB (Matlab R2023a) using advanced methods, including Partial Least Squares (PLS), Partial Least Squares Discriminant Analysis (PLS-DA), Support Vector Machines (SVM), Machine Learning, and Artificial Neural Networks (ANN), applied to NIR spectra data. The PLS, iPLS, siPLS and mwPLS models were performed using MATLAB software and the iToolbox for MATLAB available from (http://www.models.life.ku.dk/itoolbox). The Classification toolbox (version 2.0), developed by Milano Chemometrics and QSAR Research Group (http//michem.disat.unimib.it/chm), was used for classification procedure. This dataset includes the following components: 1. AMYLOSE_MODEL_FOOD_CHEMISTRY A MATLAB-based predictive model for determining rice amylose content using NIR spectroscopy combined with PLS chemometric algorithms. 2. PLS-DA_SVM_MODELS MATLAB-based predictive models for identifying different rice flour types using NIR spectroscopy with PLS-DA and SVM methods. 3. ANN_MODELS_ApSci MATLAB-based predictive models for determining rice pasting parameters using NIR spectroscopy and Machine Learning tools. 4. ANN_MODELS_PASTING_FOODS A MATLAB-based predictive model for evaluating rice quality based on grain physical parameters using Artificial Neural Network methods. The .mat files are provided in a compressed .rar format and include the models with model performance metrics, ensuring reproducibility and facilitating model evaluation.
DOI: 10.34636/dmportal/q5grto/idslxa
title: 1-AMYLOSE_MODEL_FOOD_CHEMISTRY.rar

description: MATLAB-based predictive model for determining rice amylose content using NIR spectroscopy combined with PLS chemometric algorithms
DOI: 10.34636/dmportal/q5grto/n48nqj
title: 3-ANN_MODELS_ApSci.rar

description: MATLAB-based predictive models for determining rice pasting parameters using NIR spectroscopy and Machine Learning tools.
DOI: 10.34636/dmportal/q5grto/qyvb1r
title: 2-PLS-DA_SVM MODELS.rar

description: MATLAB-based predictive models for identifying different rice flour types using NIR spectroscopy with PLS-DA and SVM methods.
DOI: 10.34636/dmportal/q5grto/wv82ht
title: 4-ANN_MODELS_PASTING_FOODS.rar

description: MATLAB-based predictive model for evaluating rice quality based on grain physical parameters using Artificial Neural Network methods.
DOI: 10.6084/m9.figshare.c.3818068_d3.v1
title: Additional file 3 of Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

description: Model. N. salina iNS934 model. SBML representation of the reconstructed model of N. salina. This file is compatible with SBML Level 3, Version 1, fbc ver. 2. It has been tested with COBRA Toolbox (2.0). (XML 4137 kb)
DOI: 10.6084/m9.figshare.c.3818068_d6
title: Additional file 6 of Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

description: Constraints used to predict growth rates. Measured uptake rates of nitrogen sources (Nitrate/ammonium/urea) and estimated CO 2 uptake rates for batch cultures of N. salina. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.c.3818092_d2
title: Additional file 2: Table S1. of Identification of long non-coding RNA in the horse transcriptome

description: The equine and corresponding human IDs of 50 lncRNA showing positional conservation to the same gene. (TXT 2Â kb)
DOI: 10.6084/m9.figshare.c.3818095_d1
title: MOESM1 of Data driven polypharmacological drug design for lung cancer: analyses for targeting ALK, MET, and EGFR

description: Additional file 1: Compound_SMILES_strings.rtf. SMILES strings for compounds tested in this manuscript (Figure 11).