cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10049856
title: AFM-ice-Au(111)-bilayer

description: Machine learning dataset of probe particle model CO-tip atomic force microscopy (AFM) simulation images of bilayer ice clusters on the Au(111) surface and the corresponding atomic structure files.
The dataset consists of a total of 1198 different structures which are divided into training, validation, and test sets as 958/72/168, and for each structure the simulations are performed 10 times with different randomized simulation parameters to yield a total of 11980 simulations. Each simulation consist of 15 images at different tip-sample distances at 0.1Å step.
The dataset is saved in a compressed .tar.gz archive. The decompressed archive has samples stored in the webdataset shard format. Each shard is a tar file with a number of samples. The tar files are named in the format `Ice-K-{param}_{set}_{shard}.tar`, where {param} number stands for the different sets of randomized simulation parameters, {set} stands for either train, validation, or test set, and {shard} is the shard number.
Each sample consists of a number of AFM simulation images and an xyz structure file. The image files are named in the format `{x}.{y}.png`, where {x} is the sample number, {y} is the index for the different height slices in the simulations. The height slices are numbered from 0 to 14, such that 0 is the farthest distance and 14 is the closest distance. Similarly, the corresponding xyz structure files are named `{x}.xyz`. The comment line (second line) in the xyz files has information about the parameters used for in the simulation for the sample.
The ice structures were obtained from a neural-network potential optimization, and subsequently the Hartree potentials for the structures were obtained through a density functional theory calculation using the optB86b-vdW density functional in Vienna Ab-initio Simulation Package. The AFM simulations utilize the Lennard-Jones force field for the Pauli repulsion and van der Waals interactions and tip convolution with the Hartree potential for the electrostatic interaction.
DOI: 10.6084/m9.figshare.7132544.v1
title: Additional file 8: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: List of plasmids downloaded from Genbank. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.7132433.v1
title: Additional file 7: of Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats

description: Table S7. Biological processes (BP) result of the downregulated differentially expressed genes (DEGs) in chronic constriction injury (CCI) model rats. (XLS 52Â kb)
DOI: 10.6084/m9.figshare.7132442.v1
title: Additional file 1: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: List of 176 isolates included in this study and the associated metadata. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.7132556
title: Additional file 9: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: List of outbreak isolates. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.21285876
title: Additional file 10 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 10. 1430 genes that are significantly regulated between EBP and Ctrl but not between EB and Ctrl.
DOI: 10.6084/m9.figshare.7132310.v1
title: Additional file 3: of Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple

description: Table S3. Promoter analyses of MdFKBPs. (XLSX 69 kb)
DOI: 10.6084/m9.figshare.7132682.v1
title: Additional file 2: of MiR-452 promotes an aggressive colorectal cancer phenotype by regulating a Wnt/Î˛-catenin positive feedback loop

description: Supplemental files. (ZIP 13000 kb)
DOI: 10.6084/m9.figshare.7132511.v1
title: Additional file 6: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: Presence-absence matrix of eight genes across isolates in this study. Serotype, CC or ST, and the presence of a plasmid is indicated for each genome. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7132556.v1
title: Additional file 9: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: List of outbreak isolates. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.18666679
title: Additional file 1 of A signature of saliva-derived exosomal small RNAs as predicting biomarker for esophageal carcinoma: a multicenter prospective study

description: Additional file 1.
DOI: 10.6084/m9.figshare.7132346
title: Additional file 2: of Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats

description: Table S2. All expressed genes in chronic constriction injury (CCI) model rats. (XLSX 2944Â kb)
DOI: 10.5281/zenodo.10554914
title: Raw Nanopore FASTQ reads from Listeria Monocytogenes strain ATCC_19112
DOI: 10.5281/zenodo.10650052
title: Raw Nanopore FASTQ reads and simulated Illumina FASTQ reads from Listeria Monocytogenes strain ATCC_19112
DOI: 10.6084/m9.figshare.7132361.v1
title: Additional file 3: of Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats

description: Table S3. Differentially expressed genes (DEGs) in chronic constriction injury (CCI) model rats. (XLSX 19Â kb)
DOI: 10.5281/zenodo.10554913
title: Raw Nanopore FASTQ reads and simulated Illumina FASTQ reads from Listeria Monocytogenes strain ATCC_19112
DOI: 10.5281/zenodo.10619642
title: Raw Nanopore FASTQ reads from Listeria Monocytogenes strain ATCC_19112
DOI: 10.6084/m9.figshare.7132682
title: Additional file 2: of MiR-452 promotes an aggressive colorectal cancer phenotype by regulating a Wnt/Î˛-catenin positive feedback loop

description: Supplemental files. (ZIP 13000 kb)
DOI: 10.6084/m9.figshare.7132382
title: Additional file 8: of Genome-wide analyses of genes encoding FK506-binding proteins reveal their involvement in abiotic stress responses in apple

description: Table S8. MdFKBP62a and MdFKBP65a/b interaction network in String10.0. (XLSX 29 kb)
DOI: 10.6084/m9.figshare.7132433
title: Additional file 7: of Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats

description: Table S7. Biological processes (BP) result of the downregulated differentially expressed genes (DEGs) in chronic constriction injury (CCI) model rats. (XLS 52Â kb)
DOI: 10.6084/m9.figshare.7132463
title: Additional file 9: of Analyses of gene expression profiles in the rat dorsal horn of the spinal cord using RNA sequencing in chronic constriction injury rats

description: Table S9. Molecular function (MF) result of the downregulated differentially expressed genes (DEGs) in chronic constriction injury (CCI) model rats. (XLS 29Â kb)
DOI: 10.6084/m9.figshare.7132496.v1
title: Additional file 5: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: Chi-Square test for significant gene clusters in lineage II. (XLSX 49 kb)
DOI: 10.6084/m9.figshare.9229841.v1
title: Projected provincial urbanization rate for China

description: Projected provincial urbanization rate for China under SSPs from 2010 to 2100
DOI: 10.6084/m9.figshare.21285876.v1
title: Additional file 10 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 10. 1430 genes that are significantly regulated between EBP and Ctrl but not between EB and Ctrl.
DOI: 10.6084/m9.figshare.21285879.v1
title: Additional file 11 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 11. qPCR Primer list.
DOI: 10.6084/m9.figshare.12899954.v1
title: Analysis of the differential expression profile of miRNAs in myocardial tissues of rats with burn injury

description: Fifteen percent third-degree burn rat model was used to identify miRNAs that are markers of burn injury-induced myocardial damage. Cardiac tissues were evaluated to determine miRNA profile sequencing. Pearson’s correlation analysis was used between miRNAs and injury markers. ROC curve analysis was used to estimate miRNA’s sensitivity and specificity for the diagnosis of myocardial damage caused by burn injury. The sequencing analysis revealed 23 differentially expressed miRNAs. Pearson’s correlation analysis revealed that rno-miR-190b-3p and C5b9, rno-miR-341, rno-miR-344b-3p and TnI, rno-miR-344b-3p and CK-MB were significantly positively correlated, respectively. ROC curve analysis demonstrated that rno-miR-341, rno-miR-344b-3p, and rno-miR-190b-3p exhibited high sensitivity and specificity for the diagnosis of myocardial damage caused by burn injury. In conclusion, our results suggest that rno-miR-341, rno-miR-344b-3p, and rno-miR-190b-3p have the potential to be used as sensitive and specific biomarkers to diagnose myocardial damage caused by burn injury. Validation of candidate miRNAs and correlation analysis Validation of candidate miRNAs and correlation analysis
DOI: 10.6084/m9.figshare.21285900.v1
title: Additional file 7 of Activation function 1 of progesterone receptor is required for progesterone antagonism of oestrogen action in the uterus

description: Additional file 7. G2M_checkpoint and E2F_Targets are not in the Top 20 gene sets enriched in EBP group vs Ctrl.
DOI: 10.6084/m9.figshare.7132532.v1
title: Additional file 7: of Genes significantly associated with lineage II food isolates of Listeria monocytogenes

description: List of eight significant genes, their homologues, and sequence accessions. (XLSX 18 kb)
DOI: 10.6084/m9.figshare.12899954
title: Analysis of the differential expression profile of miRNAs in myocardial tissues of rats with burn injury

description: Fifteen percent third-degree burn rat model was used to identify miRNAs that are markers of burn injury-induced myocardial damage. Cardiac tissues were evaluated to determine miRNA profile sequencing. Pearson’s correlation analysis was used between miRNAs and injury markers. ROC curve analysis was used to estimate miRNA’s sensitivity and specificity for the diagnosis of myocardial damage caused by burn injury. The sequencing analysis revealed 23 differentially expressed miRNAs. Pearson’s correlation analysis revealed that rno-miR-190b-3p and C5b9, rno-miR-341, rno-miR-344b-3p and TnI, rno-miR-344b-3p and CK-MB were significantly positively correlated, respectively. ROC curve analysis demonstrated that rno-miR-341, rno-miR-344b-3p, and rno-miR-190b-3p exhibited high sensitivity and specificity for the diagnosis of myocardial damage caused by burn injury. In conclusion, our results suggest that rno-miR-341, rno-miR-344b-3p, and rno-miR-190b-3p have the potential to be used as sensitive and specific biomarkers to diagnose myocardial damage caused by burn injury. Validation of candidate miRNAs and correlation analysis Validation of candidate miRNAs and correlation analysis
DOI: 10.6084/m9.figshare.12900065
title: Additional file 6 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 6: Table S5. Detailed information of 16S rRNA genes amplicon samples used in this study.
DOI: 10.6084/m9.figshare.12900059
title: Additional file 4 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 4: Table S3. Detailed genes information for figure 4.
DOI: 10.6084/m9.figshare.12900068.v1
title: Additional file 7 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 7: Table S6. Detailed information of the representative 16S rRNA gene sequences.
DOI: 10.6084/m9.figshare.12900053
title: Additional file 2 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 2: Table S1. Detailed information of organisms on the phylogenetic tree
DOI: 10.6084/m9.figshare.16569913
title: Additional file 3 of Sulfarotene, a synthetic retinoid, overcomes stemness and sorafenib resistance of hepatocellular carcinoma via suppressing SOS2-RAS pathway

description: Additional file 3: Supplementary Data 2. The association of SOS2 and associated neighboring genes.
DOI: 10.6084/m9.figshare.12900164
title: Additional file 2 of Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions

description: Additional file 2: Table S1. The primers used for identifying potential off-target sites in this study.
DOI: 10.6084/m9.figshare.14443191.v1
title: Additional file 9 of Genome sequencing and comparative genomic analysis of highly and weakly aggressive strains of Sclerotium rolfsii, the causal agent of peanut stem rot

description: Additional file 9: Table S2. Comparison of gene families of GP3, ZY, and other species in Agaricomycetes
DOI: 10.34740/kaggle/dsv/7635632
title: Batik Nusantara (Batik Indonesia) Dataset
DOI: 10.6084/m9.figshare.25232381
title: Data for npj digital medicine.zip

description: Data for npj digital medicine.The excel file like: All data\Original data\Data\\ for figure.xlsx" is the actual value of each data plot of figure 4 in the published article.Contact the corresponding author of the article if you have any questions.
DOI: 10.6084/m9.figshare.9229841
title: Projected provincial urbanization rate for China

description: Projected provincial urbanization rate for China under SSPs from 2010 to 2100
DOI: 10.6084/m9.figshare.12900130
title: Additional file 1 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 1: Table S1. RNA samples for jute (C. capsularis) in this study.
DOI: 10.6084/m9.figshare.12900127.v1
title: Additional file 15 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 15: Table S9. Expression levels of several secondary cell wall biosynthesis genes from the elite cultivar “Huangma 179” and GA3 sensitive dwarf germplasm “Aidianyehuangma” in response to GA3 stress.
DOI: 10.6084/m9.figshare.12900133
title: Additional file 2 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 2: Table S2. Summary statistics of the transcriptome sequence of jute.
DOI: 10.6084/m9.figshare.12900142.v1
title: Additional file 5 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 5: Table S5. Unigenes annotation in the public databases.
DOI: 10.6084/m9.figshare.12900145.v1
title: Additional file 6 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 6: Table S6. Annotated unigenes in the Nr databases.
DOI: 10.6084/m9.figshare.16569910
title: Additional file 2 of Sulfarotene, a synthetic retinoid, overcomes stemness and sorafenib resistance of hepatocellular carcinoma via suppressing SOS2-RAS pathway

description: Additional file 2: Supplementary Data 1. The critical genes clustered in response to sulfarotene and in association with RARα.
DOI: 10.6084/m9.figshare.16569910.v1
title: Additional file 2 of Sulfarotene, a synthetic retinoid, overcomes stemness and sorafenib resistance of hepatocellular carcinoma via suppressing SOS2-RAS pathway

description: Additional file 2: Supplementary Data 1. The critical genes clustered in response to sulfarotene and in association with RARα.
DOI: 10.6084/m9.figshare.12900065.v1
title: Additional file 6 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 6: Table S5. Detailed information of 16S rRNA genes amplicon samples used in this study.
DOI: 10.6084/m9.figshare.16569913.v1
title: Additional file 3 of Sulfarotene, a synthetic retinoid, overcomes stemness and sorafenib resistance of hepatocellular carcinoma via suppressing SOS2-RAS pathway

description: Additional file 3: Supplementary Data 2. The association of SOS2 and associated neighboring genes.
DOI: 10.6084/m9.figshare.12900121
title: Additional file 13 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 13: Table S8. Expression levels of CcWRKYs from the elite cultivar “Huangma 179” and GA3 sensitive dwarf germplasm “Aidianyehuangma” in response to GA3 stress.
DOI: 10.6084/m9.figshare.12900056
title: Additional file 3 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 3: Table S2. Detailed genes information for figure 3.
DOI: 10.6084/m9.figshare.12900059.v1
title: Additional file 4 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 4: Table S3. Detailed genes information for figure 4.
DOI: 10.6084/m9.figshare.12900127
title: Additional file 15 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 15: Table S9. Expression levels of several secondary cell wall biosynthesis genes from the elite cultivar “Huangma 179” and GA3 sensitive dwarf germplasm “Aidianyehuangma” in response to GA3 stress.
DOI: 10.6084/m9.figshare.12900062.v1
title: Additional file 5 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 5: Table S4. Detailed key genes expression changed during predation.
DOI: 10.6084/m9.figshare.12900176.v1
title: Additional file 12 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 12: Table S5. Primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.16570109
title: Additional file 1 of Circulating MiR-1290 as a potential diagnostic and disease monitoring biomarker of human gastrointestinal tumors

description: Additional file 1 : Table S1. Highly expressed serum miRNAs in patients with CRC compared to normal controls. Table S2. Different RNA extraction technologies utilized in this study. Table S3. Mean Cq values and SD of circulating miR-1290 measured by RT-qPCR in 20 healthy individuals with different RNA extraction methods. Table S4. Recovery efficiency and the influence of common interference factors. Fig. S1. Functional enrichment analysis of target genes and phylogenetic analysis of miRNAs. (a-b) GO term enrichment analysis and KEGG pathway analysis of target genes. Top three terms with FDR &lt; 0.01. (c) The phylogenetic tree of miRNAs shown in Table S1 based on the p distance and the average method. Fig. S2. The interaction regulatory network of the selected upregulated miRNAs and downregulated target mRNAs. The red circle represents miRNA, and the blue rectangle represents the target genes.
DOI: 10.25387/g3.12899993
title: Supplemental Material for Zhou et al., 2020

description: The DEGs of T07_T08_vs_T10_T11_T12
DOI: 10.6084/m9.figshare.14471412
title: Additional file 11 of Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

description: Additional file 11: Table S10. List of 75 granule cell marker genes and hippocampal CpG DMRs that overlap granule cell marker genes or their promoters.
DOI: 10.25387/g3.12899993.v1
title: Supplemental Material for Zhou et al., 2020

description: The DEGs of T07_T08_vs_T10_T11_T12
DOI: 10.6084/m9.figshare.12900136
title: Additional file 3 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 3: Table S3. Transcripts and Unigenes length interval and their distributions.
DOI: 10.6084/m9.figshare.12900136.v1
title: Additional file 3 of De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis)

description: Additional file 3: Table S3. Transcripts and Unigenes length interval and their distributions.
DOI: 10.6084/m9.figshare.12900053.v1
title: Additional file 2 of Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments

description: Additional file 2: Table S1. Detailed information of organisms on the phylogenetic tree
DOI: 10.6084/m9.figshare.14471421.v1
title: Additional file 14 of Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

description: Additional file 14: Table S13. Lists of VMRs identified in each tissue.
DOI: 10.6084/m9.figshare.12900185
title: Additional file 3 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 3: Table S3. Detected metabolites and relative content.
DOI: 10.6084/m9.figshare.14471412.v1
title: Additional file 11 of Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits

description: Additional file 11: Table S10. List of 75 granule cell marker genes and hippocampal CpG DMRs that overlap granule cell marker genes or their promoters.
DOI: 10.6084/m9.figshare.12900164.v1
title: Additional file 2 of Precise base editing with CC context-specificity using engineered human APOBEC3G-nCas9 fusions

description: Additional file 2: Table S1. The primers used for identifying potential off-target sites in this study.
DOI: 10.6084/m9.figshare.12900176
title: Additional file 12 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 12: Table S5. Primers used for qRT-PCR.
DOI: 10.6084/m9.figshare.12900191
title: Additional file 5 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 5: Table S4. Identification of continuously differentially expressed genes and metabolites.
DOI: 10.6084/m9.figshare.12900179
title: Additional file 1 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 1: Table S1. Summary of read mapping statistics.
DOI: 10.6084/m9.figshare.12900179.v1
title: Additional file 1 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 1: Table S1. Summary of read mapping statistics.
DOI: 10.6084/m9.figshare.12900182.v1
title: Additional file 2 of Dynamic transcriptome and metabolome analyses of two types of rice during the seed germination and young seedling growth stages

description: Additional file 2: Table S2. Gene expression data and annotations. All DEGs of 02428. All DEGs of YZX. Intersection of 02428 and YZX.