cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11775930
title: Additional file 4 of An open-source video tracking system for mouse locomotor activity analysis

description: Additional file 4. A sample MATLAB data output of the MouseActivity program after completing the tracking process of a movie, which include the position coordinates and area of each mouse.
DOI: 10.6084/m9.figshare.11775930.v1
title: Additional file 4 of An open-source video tracking system for mouse locomotor activity analysis

description: Additional file 4. A sample MATLAB data output of the MouseActivity program after completing the tracking process of a movie, which include the position coordinates and area of each mouse.
DOI: 10.6084/m9.figshare.14903711
title: Additional file 4 of SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer’s disease

description: Additional file 4: Suppl. Table S6. Peptide counts in subcellular fractions
DOI: 10.6084/m9.figshare.11775939
title: Additional file 8 of Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

description: Additional file 8: Table S5. Gene functional classes of protein species only detected in our comparative proteomics
DOI: 10.6084/m9.figshare.23299001
title: Additional file 3 of Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

description: Additional file 3: Data S1. Genomic regions with at least 5 SNP BSGS from a single breed. This file contains detailed information on genomic segments with at least 5 SNP BSGS from a single breed. Segments were grouped and sorted by breed.
DOI: 10.6084/m9.figshare.11775939.v1
title: Additional file 8 of Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

description: Additional file 8: Table S5. Gene functional classes of protein species only detected in our comparative proteomics
DOI: 10.6084/m9.figshare.23299004.v1
title: Additional file 4 of Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

description: Additional file 4: Data S2. SNP GS discovered across the genome. This file contains information on all genome-wide SNP GS discovered from 76 valid breeds.
DOI: 10.6084/m9.figshare.3376285.v1
title: The circadian clock regulates autophagy directly through the nuclear hormone receptor Nr1d1/Rev-erbα and indirectly via Cebpb/(C/ebpβ) in zebrafish

description: Autophagy is a highly conserved intracellular degradation system, and recently was shown to display circadian rhythms in mice. The mechanisms underlying circadian regulation of autophagy, however, are still unclear. Here, we observed that numbers of autophagosomes and autolysosomes exhibit daily rhythms in the zebrafish liver, and <i>cebpb/(c/ebp</i>β) and various autophagy genes are rhythmically expressed in zebrafish larvae but significantly upregulated in <i>per1b</i> and TALEN-generated <i>nr1d1/rev-erbα</i> mutant fish, indicating that both Per1b and Nr1d1 play critical roles in autophagy rhythms. Luciferase reporter and ChIP assays show that the circadian clock directly regulates autophagy genes through Nr1d1, and also regulates transcription of <i>cebpb</i> through Per1b. We also found that fasting leads to altered expression of both circadian clock genes and autophagy genes in zebrafish adult peripheral organs. Further, transcriptome analysis reveals multiple functions of Nr1d1 in zebrafish. Taken together, these findings provide evidence for how the circadian clock regulates autophagy, imply that nutritional signaling affects both circadian regulation and autophagy activities in peripheral organs, and shed light on how circadian gene mutations act through autophagy to contribute to common metabolic diseases such as obesity.
DOI: 10.6084/m9.figshare.14379383
title: Additional file 2 of PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

description: Additional file 2: Dataset S1. HIV-1 integration sites identified in patients 02006 and 06042.
DOI: 10.6084/m9.figshare.14379389
title: Additional file 4 of PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

description: Additional file 4: Dataset S3. PCIP-seq, ddPCR and validation oligos.
DOI: 10.6084/m9.figshare.11775948
title: Additional file 7 of An open-source video tracking system for mouse locomotor activity analysis

description: Additional file 7. A sample Excel file output of the MouseActivity program with the data of the mouse position, travel distance and thigmotaxis.
DOI: 10.6084/m9.figshare.11775963
title: Additional file 1 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 1: Table S1. Selected CBS variants and prediction scores for evaluation of prediction performance.
DOI: 10.6084/m9.figshare.11775963.v1
title: Additional file 1 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 1: Table S1. Selected CBS variants and prediction scores for evaluation of prediction performance.
DOI: 10.6084/m9.figshare.11775972
title: Additional file 3 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 3. DMS data. Contains all raw read counts, experimental scores, and the final imputed and refined data for each variant in each condition.
DOI: 10.6084/m9.figshare.11775972.v1
title: Additional file 3 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 3. DMS data. Contains all raw read counts, experimental scores, and the final imputed and refined data for each variant in each condition.
DOI: 10.6084/m9.figshare.11775978
title: Additional file 4 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 4: Table S2. Plasma CBS activity in vitamin B6 responder and non-responder.
DOI: 10.6084/m9.figshare.11775978.v1
title: Additional file 4 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 4: Table S2. Plasma CBS activity in vitamin B6 responder and non-responder.
DOI: 10.6084/m9.figshare.11775981
title: Additional file 5 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 5: Table S3. Relative in vitro catalytic activity for 24 CBS missense variants expressed in E. coli and their corresponding high vitamin B6 VE map fitness scores.
DOI: 10.6084/m9.figshare.11775981.v1
title: Additional file 5 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 5: Table S3. Relative in vitro catalytic activity for 24 CBS missense variants expressed in E. coli and their corresponding high vitamin B6 VE map fitness scores.
DOI: 10.6084/m9.figshare.11775987
title: Additional file 6 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 6: Table S4. Log likelihood ratios of pathogenicity and delta scores.
DOI: 10.6084/m9.figshare.11775987.v1
title: Additional file 6 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 6: Table S4. Log likelihood ratios of pathogenicity and delta scores.
DOI: 10.6084/m9.figshare.11775993
title: Additional file 7 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 7: Table S5. Patient clinical phenotypes and vitamin B6 responsiveness, and inferred activity from VE maps.
DOI: 10.6084/m9.figshare.14379389.v1
title: Additional file 4 of PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads

description: Additional file 4: Dataset S3. PCIP-seq, ddPCR and validation oligos.
DOI: 10.6084/m9.figshare.11775993.v1
title: Additional file 7 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 7: Table S5. Patient clinical phenotypes and vitamin B6 responsiveness, and inferred activity from VE maps.
DOI: 10.6084/m9.figshare.11775996
title: Additional file 8 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 8: Table S6. List of enzymes containing cofactors.
DOI: 10.6084/m9.figshare.11775996.v1
title: Additional file 8 of A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

description: Additional file 8: Table S6. List of enzymes containing cofactors.
DOI: 10.6084/m9.figshare.8105981.v1
title: Additional file 4: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S4. Number of elite alleles contained in each recombinant inbred line. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8105999
title: Additional file 7: of Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

description: Table S6. Primers used for qRT-PCR. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.11776050
title: Additional file 1 of Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows

description: Additional file 1: Table S1. Summary of the differentially methylated genes in the two libraries. A total of 494 DMRs including 61 up-methylated genes and 433 down-methylated genes were identified in the healthy and mastitic groups. Table S2. Summary of the differentially methylated genes harboring in the QTLs associated with clinical mastitis, somatic cell count and somatic. Table S3. Summary of the differentially methylated miRNAs in the two libraries. A total of 26 differentially methylated miRNAs including 8 up-methylated miRNAs and 18 down-methylated miRNAs were identified in the healthy and mastitic groups. Table S4. Summary of the differentially expressed genes in the two groups. A total of 1339 DEGs including 1094 up-regulated genes and 245 down-regulated genes were identified in the healthy and mastitic groups. Table S5. Summary of differentially methylated and expressed genes in the RRBS and RNA-seq sequencing. Table S6. The primers used for BSP and qPCR.
DOI: 10.6084/m9.figshare.11776050.v1
title: Additional file 1 of Genome-wide methylation and transcriptome of blood neutrophils reveal the roles of DNA methylation in affecting transcription of protein-coding genes and miRNAs in E. coli-infected mastitis cows

description: Additional file 1: Table S1. Summary of the differentially methylated genes in the two libraries. A total of 494 DMRs including 61 up-methylated genes and 433 down-methylated genes were identified in the healthy and mastitic groups. Table S2. Summary of the differentially methylated genes harboring in the QTLs associated with clinical mastitis, somatic cell count and somatic. Table S3. Summary of the differentially methylated miRNAs in the two libraries. A total of 26 differentially methylated miRNAs including 8 up-methylated miRNAs and 18 down-methylated miRNAs were identified in the healthy and mastitic groups. Table S4. Summary of the differentially expressed genes in the two groups. A total of 1339 DEGs including 1094 up-regulated genes and 245 down-regulated genes were identified in the healthy and mastitic groups. Table S5. Summary of differentially methylated and expressed genes in the RRBS and RNA-seq sequencing. Table S6. The primers used for BSP and qPCR.
DOI: 10.5281/zenodo.8387072
title: EXAFS and DRIFTS data collected during palladium hydride phase formation in supported palladium nanoparticles

description: The dataset contains DRIFTS and EXAFS spectra measured under identical conditions at different hydrogen partial pressures with the presence of 0.5% CO in the gas flow. The first line in DRIFTS.dat file is the wavenumber in inverse cm, the following lines are the averaged spectra measured at different conditions. The first line in EXAFS.dat file is the energy in eV, the following lines are the averaged spectra measured at different conditions. File params.dat contain information about the sample temperature (Temperature column), hydrogen partial pressure (H pressure), number of cycle (each experiment was repeated 3 times), and the descriptors of DRIFTS spectra: FWHM, Area (Square) and positions of 8 gaussians, 3 positions of the maxima assigned to On top, Bridged and Hollow geometries of adsorbed CO molecules, and structural descriptors obtained from EXAFS: Pd-Pd interatomic distances (R), coordination numbers (N) and Debye-Waller parameters (ss) with corresponding errors.
DOI: 10.5281/zenodo.8387073
title: EXAFS and DRIFTS data collected during palladium hydride phase formation in supported palladium nanoparticles

description: The dataset contains DRIFTS and EXAFS spectra measured under identical conditions at different hydrogen partial pressures with the presence of 0.5% CO in the gas flow. The first line in DRIFTS.dat file is the wavenumber in inverse cm, the following lines are the averaged spectra measured at different conditions. The first line in EXAFS.dat file is the energy in eV, the following lines are the averaged spectra measured at different conditions. File params.dat contain information about the sample temperature (Temperature column), hydrogen partial pressure (H pressure), number of cycle (each experiment was repeated 3 times), and the descriptors of DRIFTS spectra: FWHM, Area (Square) and positions of 8 gaussians, 3 positions of the maxima assigned to On top, Bridged and Hollow geometries of adsorbed CO molecules, and structural descriptors obtained from EXAFS: Pd-Pd interatomic distances (R), coordination numbers (N) and Debye-Waller parameters (ss) with corresponding errors.
DOI: 10.6084/m9.figshare.14903711.v1
title: Additional file 4 of SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer’s disease

description: Additional file 4: Suppl. Table S6. Peptide counts in subcellular fractions
DOI: 10.6084/m9.figshare.23299022
title: Additional file 10 of Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

description: Additional file 10: Data S8. All STR BSGS discovered across the genome. This file contains information on all genome-wide STR BSGS discovered from 76 valid breeds.
DOI: 10.6084/m9.figshare.7570688
title: Transmembrane G protein-coupled receptor 30 gene polymorphisms and uterine adenomyosis in Korean women

description: To compare the genetic distributions of 14G protein-coupled receptor 30 (GPR30) single-nucleotide polymorphisms (SNPs) between women with and without uterine adenomyosis. The study population comprised 69 Korean women. Uterine tissues from the adenomyosis and non-adenomyosis groups were used for DNA extraction. Pre-designed PCR/Sanger or Sequencing Primer and TaqMan<sup>®</sup> SNP Genotyping Assays were used for the SNP genotyping of the GPR30 gene. Immunohistochemical staining was performed to confirm the GPR30 expression. Differences in genotype and allele frequencies between the two groups were calculated using Fisher’s exact test. The rs3802141 CT genotype was more common in the control group (<i>p</i> = .02), and the rs4266553 CC genotype was more common in the adenomyosis group (<i>p</i> = .02). The C allele of the SNP rs4266553 was more common in the adenomyosis group (<i>p</i> = .02). GPR30 expression was confirmed in 69 individuals in both groups. GPR30 gene polymorphism is presumed to affect the risk of adenomyosis with limited sample size. Further large-scale study is needed to explain the genetic influence of GPR30 gene polymorphism.
DOI: 10.6084/m9.figshare.7570688.v1
title: Transmembrane G protein-coupled receptor 30 gene polymorphisms and uterine adenomyosis in Korean women

description: To compare the genetic distributions of 14G protein-coupled receptor 30 (GPR30) single-nucleotide polymorphisms (SNPs) between women with and without uterine adenomyosis. The study population comprised 69 Korean women. Uterine tissues from the adenomyosis and non-adenomyosis groups were used for DNA extraction. Pre-designed PCR/Sanger or Sequencing Primer and TaqMan<sup>®</sup> SNP Genotyping Assays were used for the SNP genotyping of the GPR30 gene. Immunohistochemical staining was performed to confirm the GPR30 expression. Differences in genotype and allele frequencies between the two groups were calculated using Fisher’s exact test. The rs3802141 CT genotype was more common in the control group (<i>p</i> = .02), and the rs4266553 CC genotype was more common in the adenomyosis group (<i>p</i> = .02). The C allele of the SNP rs4266553 was more common in the adenomyosis group (<i>p</i> = .02). GPR30 expression was confirmed in 69 individuals in both groups. GPR30 gene polymorphism is presumed to affect the risk of adenomyosis with limited sample size. Further large-scale study is needed to explain the genetic influence of GPR30 gene polymorphism.
DOI: 10.6084/m9.figshare.7570475.v1
title: Additional file 10: of Intratumor heterogeneity comparison among different subtypes of non-small-cell lung cancer through multi-region tissue and matched ctDNA sequencing

description: Supplementary Sequencing datasets. (XLSX 416 kb)
DOI: 10.6084/m9.figshare.23299025.v1
title: Additional file 11 of Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

description: Additional file 11: Data S9. Detailed list of 10-kb-long genomic block with enriched SNP GS signals. This is the summarized data used for generating Fig 2. Information on genes overlapped with each highlighted 10kb block was presented in the last column.
DOI: 10.23729/298dc155-fa23-4502-ac67-fd596dc5faad
title: JYFL-ACCLAB-JR160 Study of the B4/2 anomaly in neutron deficient Os isotopes
title: JYFL-ACCLAB-JR160 Study of the B4/2 anomaly in neutron deficient Os isotopes

description: Spokespersons: M. Doncel, T. Grahn
Liaison: T. Grahn
Date: 13.2.-20.2.2023

Beam: 78Kr15+
Beam energy [MeV]: 360 MeV
Beam current [pnA]: varied 1-2.5 pnA depending on the plunger distance.

Target: 92Mo
Target thickness [mg/cm2]: 1.3

Instrumentation: APPA plunger with natMg 1 mg/cm2 degrader foil, JG3/15 Phase I, RITU + focal plane Ge & DSSD. Recoil speed v/c=4.25% after the target

RITU dipole field [T]: 0.7874
RITU He pressure [mbar]: 0.7
RITU DSSD thickness [μm]: 300

Plunger distances used: 2, 20 60, 110, 190, 290, 390, 590, 790, 1990 μm.

Note: The cross section for 165Os (~5 μm based on α-particle yield) was found to be too low in order to record decent statistics in the present experiment. Therefore we concentrated on 167Os. Good dataset was collected for that.
DOI: 10.6084/m9.figshare.8094764
title: Association between testosterone with type 2 diabetes in adult males, a meta-analysis and trial sequential analysis

description: We performed this meta-analysis to assess serum testosterone changes in adult males with Type 2 diabetes (T2DM). PubMed, Embase, Web of Science, and Cochrane Library were searched to identify qualified studies. Pooled weighted mean differences (WMDs) with 95% confidence intervals (CIs) were utilized to test the changes of total testosterone (TT), free testosterone (FT) and sex hormone-binding globulin (SHBG) in patients with T2DM. Besides, trial sequential analysis was used to verify the pooled results. A total of 56 studies were enrolled in our meta-analysis. Meta-analyses of the cross-sectional studies showed that patients with T2DM has significant decreases in TT (WMD: −2.98, 95%CI: −3.48 to −2.47), FT (WMD: −32.82, 95%CI: −39.70 to −25.95) and SHBG (WMD: −2.47, 95%CI: −3.93 to −1.02). In terms of the prospective studies, our results showed decreases in TT (WMD: −2.35, 95%CI: −3.24 to −1.46), FT (WMD: −25.96, 95%CI: −83.98 to 32.05), and SHBG (WMD: −10.06, 95%CI: −13.29 to −6.84) in patients with T2DM. By trial sequential analyses, the findings in current meta-analysis were based on reliable evidence. Our results indicate that patients with T2DM have lower serum TT, FT, and SHBG levels.
DOI: 10.6084/m9.figshare.12813603.v1
title: Additional file 2 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 2: Table S1. Differentially expressed lncRNAs and mRNAs between GBM samples and normal brain samples in GSE51146.
DOI: 10.6084/m9.figshare.12813612.v1
title: Additional file 5 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 5: Table S4. The node degree of lncRNAs and mRNAs in Pink module.
DOI: 10.6084/m9.figshare.12813621
title: Additional file 8 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 8: Table S6. GO and KEGG enrichment for the mRNAs involved in the ceRNA network.
DOI: 10.6084/m9.figshare.12813621.v1
title: Additional file 8 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 8: Table S6. GO and KEGG enrichment for the mRNAs involved in the ceRNA network.
DOI: 10.6084/m9.figshare.12813603
title: Additional file 2 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 2: Table S1. Differentially expressed lncRNAs and mRNAs between GBM samples and normal brain samples in GSE51146.
DOI: 10.6084/m9.figshare.12813609
title: Additional file 4 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 4: Table S3. Co-expression of Pink module between lncRNAs and mRNAs.
DOI: 10.6084/m9.figshare.12813618.v1
title: Additional file 7 of Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme

description: Additional file 7: Table S5. The lncRNA-miRNA-mRNA ceRNA network.
DOI: 10.6084/m9.figshare.14903874
title: Additional file 1 of Trends in breastfeeding practices and mothers’ experience in the French NutriNet-Santé cohort

description: Additional file 1. Mothers’ perceptions on (A) breastfeeding cessation and (B) support to breastfeeding cessation. Self-reported mothers’ perceptions about factors known to have an impact on (A) breastfeeding cessation (B) support to breastfeeding cessation, but that were not felt by mothers to have played a role. Results are percentages of answers. Mothers had choice to answer from totally agree to totally disagree for each item (see legend); a not applicable answer was possible if the item was not adapted to the mother’s life.
DOI: 10.6084/m9.figshare.12813631.v1
title: Additional file 2 of Functional analysis of the SlERF01 gene in disease resistance to S. lycopersici

description: Additional file 2: Table S2.
DOI: 10.6084/m9.figshare.14379495.v1
title: Additional file 2 of Genome-scale analyses of transcriptional start sites in Mycobacterium marinum under normoxic and hypoxic conditions

description: Additional file 2.