cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.c.3661790_d7.v1
title: Additional file 3: Table S2. of Functional changes in mRNA expression and alternative pre-mRNA splicing associated with the effects of nutrition on apoptosis and spermatogenesis in the adult testis

description: Differentially expressed mRNAs in testis from sheep fed a low or high diet (N = 8 for each treatment). Note: Fold change (FC) = CPM of low diet group/CPM of high diet group. CPM (Counts per million) = (mRNAs reads number/total reads number per library) Ă  1,000,000. The significant DE mRNAs were determined by false discovery rate (FDR) &lt; 0.05. (XLSX 168 kb)
DOI: 10.6084/m9.figshare.28049978
title: Narcissus pseudonarcissus raw GC-MS files

description: Metabolite extraction from Narcissus pseudonarcissus leaf tissue
DOI: 10.6084/m9.figshare.28049978.v1
title: Narcissus pseudonarcissus raw GC-MS files

description: Metabolite extraction from Narcissus pseudonarcissus leaf tissue
DOI: 10.6084/m9.figshare.c.3661862_d1.v1
title: MOESM3 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

description: Additional file 3: Table S2. Normalized spectral abundance factor (NSAF) normalized protein spectral count measurements using mass spectrometry.
DOI: 10.6084/m9.figshare.c.3661862_d1
title: MOESM3 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

description: Additional file 3: Table S2. Normalized spectral abundance factor (NSAF) normalized protein spectral count measurements using mass spectrometry.
DOI: 10.6084/m9.figshare.c.3661856_d1
title: Additional file 1: of Toward a comprehensive drug ontology: extraction of drug-indication relations from diverse information sources

description: Drug-Indication Database non-proprietary subset. (XLSX 61806Â kb)
DOI: 10.6084/m9.figshare.c.3661862_d4.v1
title: MOESM6 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

description: Additional file 6: Table S5. The comparison table of position preference, gene expression and MS detected proteins.
DOI: 10.6084/m9.figshare.c.3661862_d4
title: MOESM6 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

description: Additional file 6: Table S5. The comparison table of position preference, gene expression and MS detected proteins.
DOI: 10.6084/m9.figshare.c.3661862_d5.v1
title: MOESM7 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

description: Additional file 7: Table S6. Significantly time-dependent (pÂ
DOI: 10.6084/m9.figshare.c.3661862_d5
title: MOESM7 of Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass

description: Additional file 7: Table S6. Significantly time-dependent (pÂ
DOI: 10.15468/dl.sjdtrq
title: Occurrence Download

description: A dataset containing 4416 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amaranthus tuberculatus (Moq.) J.D.Sauer"
 ]
}

 The dataset includes 4416 records from 164 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0038080-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25919/dnah-6985
title: Parkes observations for project P1317 semester 2024OCTS_02

description: The existence of a population of millisecond pulsars (MSPs) in the Galactic bulge is supported, among others, by the Fermi GeV excess, a signal of gamma rays coming from the Galactic center (GC) direction and resembling the cumulative emission of known MSPs. A previous study showed that, while these MSPs are unresolved in gamma rays, some of them could have been detected in past X-ray observations. The authors also identified a large number of MSP candidates among unidentified X-ray sources. By analyzing unpublished radio images, we found interesting radio counterparts to 6 of those candidates, and were granted 20h of observations with the Green Bank Telescope to settle on their nature. We discovered two new MSPs, PSR J1740-2807 and PSR J1740-2805, towards one of our radio/X-ray targets, bringing to 4 the number of highly-dispersed MSPs in the GC direction and probably unveiling the first direct evidence of a bulge MSP population. We propose to carry out regular timing of these pulsar with Parkes, in order to reveal their properties and potentially claim association of PSR J1740-2807 with the original X-ray source. The follow up of these sources will have a major impact on our understanding of the Fermi GeV excess.
DOI: 10.6084/m9.figshare.c.3661877_d2.v1
title: Additional file 1: of Outcome-sensitive multiple imputation: a simulation study

description: Simulation code file 1 of 4. Generate data and obtain true estimates (making sure the simulations work as they should before incorporating the missing data mechanisms). Simulation code file 2 of 4. Main data generation file across missingness mechanisms (1 of 2). Simulation code file 3 of 4. Main data generation file across missingness mechanisms (2 of 2). Simulation code file 4 of 4. Summarise the simulation results in a data file. (ZIP 10Â kb)
DOI: 10.6084/m9.figshare.c.3661877_d2
title: Additional file 1: of Outcome-sensitive multiple imputation: a simulation study

description: Simulation code file 1 of 4. Generate data and obtain true estimates (making sure the simulations work as they should before incorporating the missing data mechanisms). Simulation code file 2 of 4. Main data generation file across missingness mechanisms (1 of 2). Simulation code file 3 of 4. Main data generation file across missingness mechanisms (2 of 2). Simulation code file 4 of 4. Summarise the simulation results in a data file. (ZIP 10Â kb)
DOI: 10.6084/m9.figshare.c.3662702_d2.v1
title: Additional file 6: of A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

description: FASTA predicted proteins of C. graminicola strain M5.001. (TXT 7838Â kb)
DOI: 10.6084/m9.figshare.c.3662702_d2
title: Additional file 6: of A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

description: FASTA predicted proteins of C. graminicola strain M5.001. (TXT 7838Â kb)
DOI: 10.6084/m9.figshare.c.3662744_d1.v1
title: Additional file 2: Supplementary Tables: Table S1. of Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress

description: Statistical comparisons of Bray-Curtis distances between a priori groupings. Related to Figure 4. Table S2. discriminatory OTUs between undefeated vehicle- and JB-1-treated controls, and vehicle- and JB-1-treated defeated mice. Related to Figure 4. Table S3. fecal metabolites altered in response to stress. Table S4. Main effect of L. rhamnosus (JB-1) treatment on fecal metabolites. Table S5. fecal metabolites altered by stress (DEF/VEH vs CON/VEH) but unaffected in DEF/JB-1 vs CON/VEH. Related to Figure 5. Table S6. Primer sequences used for real time quantitative PCR. Related to Figure S2. (XLSX 83 kb)
DOI: 10.6084/m9.figshare.c.3662741_d2.v1
title: Additional file 6: of Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

description: Genotypic data. Genotypes of 580 individuals of P. margaritifera at 10,683 adaptive and selectively neutral genome-wide SNPs are included in a standard STRUCTURE format. (ZIP 2276Â kb)
DOI: 10.6084/m9.figshare.c.3662744_d1
title: Additional file 2: Supplementary Tables: Table S1. of Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress

description: Statistical comparisons of Bray-Curtis distances between a priori groupings. Related to Figure 4. Table S2. discriminatory OTUs between undefeated vehicle- and JB-1-treated controls, and vehicle- and JB-1-treated defeated mice. Related to Figure 4. Table S3. fecal metabolites altered in response to stress. Table S4. Main effect of L. rhamnosus (JB-1) treatment on fecal metabolites. Table S5. fecal metabolites altered by stress (DEF/VEH vs CON/VEH) but unaffected in DEF/JB-1 vs CON/VEH. Related to Figure 5. Table S6. Primer sequences used for real time quantitative PCR. Related to Figure S2. (XLSX 83 kb)
DOI: 10.6084/m9.figshare.c.3662741_d2
title: Additional file 6: of Swept away: ocean currents and seascape features influence genetic structure across the 18,000 Km Indo-Pacific distribution of a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera

description: Genotypic data. Genotypes of 580 individuals of P. margaritifera at 10,683 adaptive and selectively neutral genome-wide SNPs are included in a standard STRUCTURE format. (ZIP 2276Â kb)
DOI: 10.6084/m9.figshare.28049981
title: Ophiopogon planiscapus raw GC-MS files

description: Metabolite extraction from Ophiopogon planiscapus leaf tissue
DOI: 10.6084/m9.figshare.28049981.v1
title: Ophiopogon planiscapus raw GC-MS files

description: Metabolite extraction from Ophiopogon planiscapus leaf tissue
DOI: 10.6084/m9.figshare.c.3662759_d2.v1
title: MOESM1 of MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

description: Additional file 1. FASTA file containing MS_HistoneDB mouse entries in a mouse Swiss-Prot FASTA file.
DOI: 10.25919/e1js-7a70
title: Parkes observations for project P1347 semester 2024OCTS_01

description: A MeerKAT imaging survey of the Galactic Center and Bulge region yielded the detections of 39 known pulsars and 30 pulsar candidates. The candidates were identified primarily as steep-spectrum, circularly- and/or linearly-polarized sources, and to a lesser degree by the level of radio variability observed. We have chosen nine pulsar candidates to target in this proposal. These sources are the most pulsar-like of the MeerKAT point sources (based on their polarization, spectral index, and variability) that also have large enough flux densities to make a firm detection of pulsations if present. We propose to observe these nine candidates twice, for 1.5 hr each, in the 2024OCT semester.
DOI: 10.6084/m9.figshare.c.3662759_d5.v1
title: MOESM5 of MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

description: Additional file 5. MS_HistoneDB human entries with links to gene, transcript and protein identifiers.
DOI: 10.6084/m9.figshare.c.3662759_d4
title: MOESM4 of MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

description: Additional file 4. MS_HistoneDB mouse entries with links to gene, transcript and protein identifiers.
DOI: 10.6084/m9.figshare.c.3662759_d5
title: MOESM5 of MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones

description: Additional file 5. MS_HistoneDB human entries with links to gene, transcript and protein identifiers.
DOI: 10.6084/m9.figshare.c.3662756_d7.v1
title: MOESM3 of Long noncoding RNA repertoire in chicken liver and adipose tissue

description: Additional file 3: Table S2. Enriched biological process GO terms of the liver- or adipose-specific subsets for protein-coding genes and long noncoding genes. The enrichment was performed using DAVID software [41, 42], and the GO terms were considered enriched according to the DAVID thresholds used by default.
DOI: 10.6084/m9.figshare.c.3662756_d7
title: MOESM3 of Long noncoding RNA repertoire in chicken liver and adipose tissue

description: Additional file 3: Table S2. Enriched biological process GO terms of the liver- or adipose-specific subsets for protein-coding genes and long noncoding genes. The enrichment was performed using DAVID software [41, 42], and the GO terms were considered enriched according to the DAVID thresholds used by default.
DOI: 10.6084/m9.figshare.c.3663445_d1.v1
title: Additional file 1: of MALAT1 promoted invasiveness of gastric adenocarcinoma

description: Cancer-related target gene expression by MALAT1 silencing. To analyze the relation among cancer-related target genes by siMALAT1, NanoString nCounter gene expression analysis was carried out. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3663448_d1.v1
title: Additional file 8: Table S7. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Methylated cytosines in brain nuclear poly(A) RNA. (XLSX 797 kb)
DOI: 10.6084/m9.figshare.c.3663448_d1
title: Additional file 8: Table S7. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Methylated cytosines in brain nuclear poly(A) RNA. (XLSX 797 kb)
DOI: 10.6084/m9.figshare.c.3663445_d1
title: Additional file 1: of MALAT1 promoted invasiveness of gastric adenocarcinoma

description: Cancer-related target gene expression by MALAT1 silencing. To analyze the relation among cancer-related target genes by siMALAT1, NanoString nCounter gene expression analysis was carried out. (XLSX 42 kb)
DOI: 10.6084/m9.figshare.c.3663448_d5.v1
title: Additional file 10: Table S9. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Primer sequences. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3663448_d5
title: Additional file 10: Table S9. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Primer sequences. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.c.3663487_d1
title: Additional file 1: of Validity of gestational age estimates by last menstrual period and neonatal examination compared to ultrasound in Vietnam

description: Analytic Dataset. (XLSX 123Â kb)
DOI: 10.6084/m9.figshare.c.3663448_d6.v1
title: Additional file 3: Table S2. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Câ  â  â  T conversion rates for spike-in controls. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3663463_d4.v1
title: Additional file 2: Table S2. of An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)

description: A. List of all detected QTLs at both significant and suggestive level for pod number. B. List of identified QTLs after deleting non-reproducible suggestive QTLs for pod number. C. Details of identified QTLs for pod number in the BnaZNRIL population in rapeseed. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3663463_d4
title: Additional file 2: Table S2. of An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)

description: A. List of all detected QTLs at both significant and suggestive level for pod number. B. List of identified QTLs after deleting non-reproducible suggestive QTLs for pod number. C. Details of identified QTLs for pod number in the BnaZNRIL population in rapeseed. (XLSX 21Â kb)
DOI: 10.6084/m9.figshare.c.3663448_d6
title: Additional file 3: Table S2. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Câ  â  â  T conversion rates for spike-in controls. (XLSX 36 kb)
DOI: 10.6084/m9.figshare.c.3663463_d5.v1
title: Additional file 4: Table S4. of An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)

description: The differentially expressed genes (DEGs) between Zhongshuang11 and No.73290 samples using false discovery rate (FDR)  2 as the significant cutoff. RPKM: reads per kilobase per million reads. (XLSX 1029 kb)
DOI: 10.6084/m9.figshare.c.3663463_d5
title: Additional file 4: Table S4. of An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)

description: The differentially expressed genes (DEGs) between Zhongshuang11 and No.73290 samples using false discovery rate (FDR)  2 as the significant cutoff. RPKM: reads per kilobase per million reads. (XLSX 1029 kb)
DOI: 10.6084/m9.figshare.c.3663448_d7.v1
title: Additional file 1: Table S1. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: General sequencing and m5C calling results. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3663448_d7
title: Additional file 1: Table S1. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: General sequencing and m5C calling results. (XLSX 34 kb)
DOI: 10.6084/m9.figshare.c.3663496_d1
title: Additional file 2: Table S1. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

description: Differentially expressed genes after BMP4 treatment in MDA-MB-231 cell line. Ensembl IDs, read counts, fold changes and Log2 ratios are shown. The genes are arranged in order from the largest to smallest Log2 ratio, first upregulated genes and then downregulated genes. (XLSX 20Â kb)
DOI: 10.6084/m9.figshare.c.3663496_d1.v1
title: Additional file 2: Table S1. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

description: Differentially expressed genes after BMP4 treatment in MDA-MB-231 cell line. Ensembl IDs, read counts, fold changes and Log2 ratios are shown. The genes are arranged in order from the largest to smallest Log2 ratio, first upregulated genes and then downregulated genes. (XLSX 20Â kb)
DOI: 10.5281/zenodo.14510962
title: Model Parameters and Test Files for T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment

description: This dataset contains all the model parameters and test files required for reproducing the results presented in the paper:

T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment.

T-ALPHA is a novel deep learning model designed to predict protein-ligand binding affinity with state-of-the-art accuracy, integrating multimodal feature representations from three distinct channels—protein, ligand, and protein-ligand complex. This dataset includes:



Model Parameters: Fully trained model weights saved during the training of the T-ALPHA architecture. These parameters are essential for inference and validation of the model's performance.

Test Files: Protein-ligand complex datasets used for evaluation, including CASF 2016, LP-PDBbind, BDB2020+, and protein-specific test sets for SARS-CoV-2 main protease (Mpro) and the epidermal growth factor receptor (EGFR). The data is processed and formatted for direct use with T-ALPHA.


These files facilitate full reproducibility of the experiments, including evaluation benchmarks, uncertainty-aware self-learning for protein-specific alignment, and generalization performance on predicted structures.
DOI: 10.5281/zenodo.14510963
title: Model Parameters and Test Files for T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment

description: This dataset contains all the model parameters and test files required for reproducing the results presented in the paper:

T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction with Uncertainty-Aware Self-Learning for Protein-Specific Alignment.

T-ALPHA is a novel deep learning model designed to predict protein-ligand binding affinity with state-of-the-art accuracy, integrating multimodal feature representations from three distinct channels—protein, ligand, and protein-ligand complex. This dataset includes:



Model Parameters: Fully trained model weights saved during the training of the T-ALPHA architecture. These parameters are essential for inference and validation of the model's performance.

Test Files: Protein-ligand complex datasets used for evaluation, including CASF 2016, LP-PDBbind, BDB2020+, and protein-specific test sets for SARS-CoV-2 main protease (Mpro) and the epidermal growth factor receptor (EGFR). The data is processed and formatted for direct use with T-ALPHA.


These files facilitate full reproducibility of the experiments, including evaluation benchmarks, uncertainty-aware self-learning for protein-specific alignment, and generalization performance on predicted structures.
DOI: 10.6084/m9.figshare.c.3663496_d3
title: Additional file 5: Table S5. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

description: Comparison between our T-47D DNase-seq data and analogous data from ENCODE. DNase-seq peaks from promoter regions in BMP4-treated and vehicle-treated T-47D cells were compared to DNase-seq data of T-47D promoters from ENCODE (ENCSR000ELT replicates 1 and 2; ENCSR000EQB replicates 1 and 2). The table shows the percentage of shared peaks between pairs of samples. A high percentage of the peaks identified in our data are also present in ENCODE samples (cells B6-E7). (XLSX 8Â kb)
DOI: 10.6084/m9.figshare.c.3663448_d10.v1
title: Additional file 9: Table S8. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Statistical analysis of m5C overlap with RNA binding protein (RBP) sequences in total poly(A) RNA of ESCs and brain. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3663448_d10
title: Additional file 9: Table S8. of Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain

description: Statistical analysis of m5C overlap with RNA binding protein (RBP) sequences in total poly(A) RNA of ESCs and brain. (XLSX 41 kb)
DOI: 10.6084/m9.figshare.c.3663505_d1.v1
title: Additional file 2: Table S2. of Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

description: Multiple T Teste performed comparing the diversity index (Shannon and Simpson) between AF Zika samples and Controls Groups. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3663505_d1
title: Additional file 2: Table S2. of Pregnant women carrying microcephaly foetuses and Zika virus contain potentially pathogenic microbes and parasites in their amniotic fluid

description: Multiple T Teste performed comparing the diversity index (Shannon and Simpson) between AF Zika samples and Controls Groups. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.c.3663496_d5
title: Additional file 4: Table S3. of Integrated RNA-seq and DNase-seq analyses identify phenotype-specific BMP4 signaling in breast cancer

description: Survival analysis of DEGs in MDA-MB-231. Table S4. Survival analysis of DEGs in T-47D. Each differentially expressed protein - coding gene was tested for possible association with the survival of breast cancer patients based on the gene expression data obtained from The Cancer Genome Atlas (TCGA). Blue background indicates DEGs shared by both cell lines. Benjamini-Hochberg corrected P-values are shown. No diff. = no association with survival. Not availableâ  =â  not found in TCGA data. (XLSX 16Â kb)