cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12212093
title: Additional file 1 of Assessing the power of principal components and wright’s fixation index analyzes applied to reveal the genome-wide genetic differences between herds of Holstein cows

description: Additional file 1: Table S1. Effect of outliers on estimates of Fst values for complete data. a - Fst values for complete data corrected on the outliers are above the diagonal and Fst values for complete data does not corrected on the outliers are below the diagonal. b - Increased Fst values are in bold and decreased Fst values are in bold Italic. Table S2. Effect of rare alleles with MAF
DOI: 10.6084/m9.figshare.12212102.v1
title: Additional file 3 of Lag penalized weighted correlation for time series clustering

description: Additional file 3 Cluster assignments and DAVID enrichment for yeast hLPWC as tab-delimited text files. The cluster assignment files contain a header row. The id is the phosphopeptide id from Kanshin et al. [32] and Uniprot is the accession number. There are no enriched terms for cluster 3.
DOI: 10.6084/m9.figshare.12212090.v1
title: Additional file 2 of Lag penalized weighted correlation for time series clustering

description: Additional file 2 Cluster assignments and DAVID enrichment for yeast lLPWC as tab-delimited text files. The cluster assignment files contain a header row. The id is the phosphopeptide id from Kanshin et al. [32] and Uniprot is the accession number.
DOI: 10.6084/m9.figshare.12212093.v1
title: Additional file 1 of Assessing the power of principal components and wright’s fixation index analyzes applied to reveal the genome-wide genetic differences between herds of Holstein cows

description: Additional file 1: Table S1. Effect of outliers on estimates of Fst values for complete data. a - Fst values for complete data corrected on the outliers are above the diagonal and Fst values for complete data does not corrected on the outliers are below the diagonal. b - Increased Fst values are in bold and decreased Fst values are in bold Italic. Table S2. Effect of rare alleles with MAF
DOI: 10.6084/m9.figshare.12211919
title: Additional file 1 of Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

description: Additional file 1: Table S1. Accession numbers of RNA-seq data used in this study. Table S2. Expression levels of ERE families in human tissues. Table S3. Tissue specificities of ERE families. Table S4. Information concerning samples used for immunopeptidomic analyses. Table S5. Characteristics of ereMAPs identified in B-LCL samples. Table S6. Characteristics of ereMAPs identified in OVCAR-3 cells.
DOI: 10.6084/m9.figshare.12211919.v1
title: Additional file 1 of Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

description: Additional file 1: Table S1. Accession numbers of RNA-seq data used in this study. Table S2. Expression levels of ERE families in human tissues. Table S3. Tissue specificities of ERE families. Table S4. Information concerning samples used for immunopeptidomic analyses. Table S5. Characteristics of ereMAPs identified in B-LCL samples. Table S6. Characteristics of ereMAPs identified in OVCAR-3 cells.
DOI: 10.6084/m9.figshare.12211868
title: Additional file 1 of Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema

description: Additional file 1: Table S1. Comparison of demographic variables between subjects included and excluded from study. Figure S1. Antibiotic resistance genotypes over time. The percentage of subjects with the antibiotic resistance genotype are presented over time. Table S2. Maternal antibiotic exposures during pregnancy. Table S3. Maternal antibiotic exposures during labour.
DOI: 10.6084/m9.figshare.12211859
title: Additional file 2 of NEK10 interactome and depletion reveal new roles in mitochondria

description: Additional file 2: Table S1. NEK10 protein interactors identified in HEK293T cells treated or not with zeocin by IP-MS/MS. Proteins marked with an asterisk: *: Retrieved from the databank by IIS platform [Carazzolle et al., 2014]. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD018294.
DOI: 10.6084/m9.figshare.12211868.v1
title: Additional file 1 of Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema

description: Additional file 1: Table S1. Comparison of demographic variables between subjects included and excluded from study. Figure S1. Antibiotic resistance genotypes over time. The percentage of subjects with the antibiotic resistance genotype are presented over time. Table S2. Maternal antibiotic exposures during pregnancy. Table S3. Maternal antibiotic exposures during labour.
DOI: 10.6084/m9.figshare.12211859.v1
title: Additional file 2 of NEK10 interactome and depletion reveal new roles in mitochondria

description: Additional file 2: Table S1. NEK10 protein interactors identified in HEK293T cells treated or not with zeocin by IP-MS/MS. Proteins marked with an asterisk: *: Retrieved from the databank by IIS platform [Carazzolle et al., 2014]. The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD018294.
DOI: 10.6084/m9.figshare.12211781
title: Additional file 4 of Comparison of Ferguson’s δ and the Gini coefficient used for measuring the inequality of data related to health quality of life outcomes

description: Additional file 4. Excel file to calculate Delta and GC as well as contents for this study.
DOI: 10.6084/m9.figshare.12211781.v1
title: Additional file 4 of Comparison of Ferguson’s δ and the Gini coefficient used for measuring the inequality of data related to health quality of life outcomes

description: Additional file 4. Excel file to calculate Delta and GC as well as contents for this study.
DOI: 10.6084/m9.figshare.12211769
title: Additional file 2 of Comparison of Ferguson’s δ and the Gini coefficient used for measuring the inequality of data related to health quality of life outcomes

description: Additional file 2. MP4 showing the simulation process http://www.healthup.org.tw/marketing/course/marketing/raschsimulateddata.mp4.
DOI: 10.6084/m9.figshare.12211763
title: Additional file 1 of Comparison of Ferguson’s δ and the Gini coefficient used for measuring the inequality of data related to health quality of life outcomes

description: Additional file 1. The process of simulation data in this study at https://youtu.be/5BLJtiif2M4.
DOI: 10.6084/m9.figshare.12211769.v1
title: Additional file 2 of Comparison of Ferguson’s δ and the Gini coefficient used for measuring the inequality of data related to health quality of life outcomes

description: Additional file 2. MP4 showing the simulation process http://www.healthup.org.tw/marketing/course/marketing/raschsimulateddata.mp4.
DOI: 10.6084/m9.figshare.12211757
title: Additional file 3 of A scoping review and proposed workflow for multi-omic rare disease research

description: Additional file 3: Table S4. List of several multi-omics.
DOI: 10.6084/m9.figshare.12211763.v1
title: Additional file 1 of Comparison of Ferguson’s δ and the Gini coefficient used for measuring the inequality of data related to health quality of life outcomes

description: Additional file 1. The process of simulation data in this study at https://youtu.be/5BLJtiif2M4.
DOI: 10.6084/m9.figshare.12211748
title: Additional file 1 of A scoping review and proposed workflow for multi-omic rare disease research

description: Additional file 1: Table S1. Full data extraction, sheet 2, abbreviations from Table S1.
DOI: 10.6084/m9.figshare.12211748.v1
title: Additional file 1 of A scoping review and proposed workflow for multi-omic rare disease research

description: Additional file 1: Table S1. Full data extraction, sheet 2, abbreviations from Table S1.
DOI: 10.6084/m9.figshare.12211757.v1
title: Additional file 3 of A scoping review and proposed workflow for multi-omic rare disease research

description: Additional file 3: Table S4. List of several multi-omics.
DOI: 10.6084/m9.figshare.12211718
title: Additional file 8 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 8: Table S6. Fungal genome sequences removed from the RefSeq fungi database (RefSeq-f-partial) to mimic the effects of classifying species without reference genomes.
DOI: 10.6084/m9.figshare.12211712
title: Additional file 7 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 7: Table S5. Genome sequences and species used to simulate fungal communities.
DOI: 10.6084/m9.figshare.12211718.v1
title: Additional file 8 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 8: Table S6. Fungal genome sequences removed from the RefSeq fungi database (RefSeq-f-partial) to mimic the effects of classifying species without reference genomes.
DOI: 10.6084/m9.figshare.12211703
title: Additional file 6 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 6: Table S4. Species observed in the metatranscriptome of wild birds (biological data set 2) and their abundance.
DOI: 10.6084/m9.figshare.12211712.v1
title: Additional file 7 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 7: Table S5. Genome sequences and species used to simulate fungal communities.
DOI: 10.6084/m9.figshare.12211694
title: Additional file 4 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 4: Table S2. Precision, recall and F1 scores obtained with the CCMetagen analysis with assembled sequence reads.
DOI: 10.6084/m9.figshare.12211700
title: Additional file 5 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 5: Table S3. Species and transcripts observed in the metatranscriptome of a mock fungal community (biological data set 1).
DOI: 10.6084/m9.figshare.12211703.v1
title: Additional file 6 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 6: Table S4. Species observed in the metatranscriptome of wild birds (biological data set 2) and their abundance.
DOI: 10.6084/m9.figshare.12211694.v1
title: Additional file 4 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 4: Table S2. Precision, recall and F1 scores obtained with the CCMetagen analysis with assembled sequence reads.
DOI: 10.6084/m9.figshare.12211700.v1
title: Additional file 5 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 5: Table S3. Species and transcripts observed in the metatranscriptome of a mock fungal community (biological data set 1).
DOI: 10.6084/m9.figshare.12211682
title: Additional file 2 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 2: Table S1. Precision, recall and F1 scores obtained for fungal communities.
DOI: 10.6084/m9.figshare.12211682.v1
title: Additional file 2 of CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

description: Additional file 2: Table S1. Precision, recall and F1 scores obtained for fungal communities.
DOI: 10.6084/m9.figshare.12211613
title: Additional file 1 of Evaluation of Domestication Loci Associated with Awnlessness in Cultivated Rice, Oryza sativa

description: Additional file 1: Table S1. Additional molecular markers used for QTL analysis and fine mapping. Table S2. Average awn lengths (mm) and standard deviation observed for the homozygous genotypes derived from the recombinants (n = 5). Table S3. List of genes annotated in a 157.4-kb candidate region of qAWNL2, by the RAP-DB.
DOI: 10.6084/m9.figshare.12211613.v1
title: Additional file 1 of Evaluation of Domestication Loci Associated with Awnlessness in Cultivated Rice, Oryza sativa

description: Additional file 1: Table S1. Additional molecular markers used for QTL analysis and fine mapping. Table S2. Average awn lengths (mm) and standard deviation observed for the homozygous genotypes derived from the recombinants (n = 5). Table S3. List of genes annotated in a 157.4-kb candidate region of qAWNL2, by the RAP-DB.
DOI: 10.6084/m9.figshare.12211580
title: Additional file 6 of Extensively drug-resistant Haemophilus influenzae – emergence, epidemiology, risk factors, and regimen

description: Additional file 6. Dataset. Dataset used in this study.
DOI: 10.6084/m9.figshare.12211580.v1
title: Additional file 6 of Extensively drug-resistant Haemophilus influenzae – emergence, epidemiology, risk factors, and regimen

description: Additional file 6. Dataset. Dataset used in this study.
DOI: 10.6084/m9.figshare.12211493
title: Additional file 1 of Validation of machine learning models to detect amyloid pathologies across institutions

description: Additional file 1. Emory cohort case information, demographics, CERAD scores, pathology diagnosis, Reagan scores, post-mortem interval, CERAD score, Braak stage, Thal stage, ABC score.
DOI: 10.6084/m9.figshare.12211493.v1
title: Additional file 1 of Validation of machine learning models to detect amyloid pathologies across institutions

description: Additional file 1. Emory cohort case information, demographics, CERAD scores, pathology diagnosis, Reagan scores, post-mortem interval, CERAD score, Braak stage, Thal stage, ABC score.
DOI: 10.6084/m9.figshare.12211364
title: Additional file 2 of Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples

description: Table S1. (A list of CpG sites with methylation patterns in Fig. 1 & Additional file 1: Figure S1). Table S2. (Sex-independent age-related CpGs from LSADT). Table S3. (Sex-independent age-related CpGs from MADT). Table S4. (Male-only age-related CpGs from LSADT). Table S5. (Male-only age-related CpGs from MADT). Table S6. (Female-only age-related CpGs from LSADT). Table S7. (Female-only age-related CpGs from MADT). Table S8. (LBC validated CpGs).
DOI: 10.6084/m9.figshare.12211364.v1
title: Additional file 2 of Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples

description: Table S1. (A list of CpG sites with methylation patterns in Fig. 1 & Additional file 1: Figure S1). Table S2. (Sex-independent age-related CpGs from LSADT). Table S3. (Sex-independent age-related CpGs from MADT). Table S4. (Male-only age-related CpGs from LSADT). Table S5. (Male-only age-related CpGs from MADT). Table S6. (Female-only age-related CpGs from LSADT). Table S7. (Female-only age-related CpGs from MADT). Table S8. (LBC validated CpGs).
DOI: 10.6084/m9.figshare.12211313
title: Additional file 2 of Urine NGAL as a biomarker for septic AKI: a critical appraisal of clinical utility—data from the observational FINNAKI study

description: Additional file 2: Correlations between the variables and multicollinearity test results.
DOI: 10.6084/m9.figshare.12211313.v1
title: Additional file 2 of Urine NGAL as a biomarker for septic AKI: a critical appraisal of clinical utility—data from the observational FINNAKI study

description: Additional file 2: Correlations between the variables and multicollinearity test results.
DOI: 10.6084/m9.figshare.12211286
title: Additional file 1 of Imaging in clinical trials: a patient-led questionnaire study to assess impact of imaging regimes on patient participation

description: Additional file 1.
DOI: 10.6084/m9.figshare.12211286.v1
title: Additional file 1 of Imaging in clinical trials: a patient-led questionnaire study to assess impact of imaging regimes on patient participation

description: Additional file 1.
DOI: 10.6084/m9.figshare.12211259
title: Additional file 2 of Uncovering the mechanism of the effects of Paeoniae Radix Alba on iron-deficiency anaemia through a network pharmacology-based strategy

description: Additional file 2: File 2a: Table 1 Known therapeutic targets for IDA; File 2b: Table 2 Targets for PRA.
DOI: 10.6084/m9.figshare.12211259.v1
title: Additional file 2 of Uncovering the mechanism of the effects of Paeoniae Radix Alba on iron-deficiency anaemia through a network pharmacology-based strategy

description: Additional file 2: File 2a: Table 1 Known therapeutic targets for IDA; File 2b: Table 2 Targets for PRA.
DOI: 10.6084/m9.figshare.12210833
title: BMI-1 expression increases in oral leukoplakias and correlates with cell proliferation

description: Abstract Oral leukoplakia (OL) is a white lesion of an indeterminate risk not related to any excluded (other) known diseases or disorders that carry no increased risk for cancer. Many biological markers have been used in an attempt to predict malignant transformation; however, no reliable markers have been established so far. Objective To evaluate cell proliferation and immortalization in OL, comparing non-dysplastic (Non-dys OL) and dysplastic OL (Dys OL). Methodology This is a cross-sectional observational study. Paraffin-embedded tissue blocks of 28 specimens of Non-dys OL, 33 of Dys OL, 9 of normal oral mucosa (NOM), 17 of inflammatory hyperplasia (IH), and 19 of oral squamous cell carcinomas (OSCC) were stained for Ki-67 and BMI-1 using immunohistochemistry. Results A gradual increase in BMI-1 and K-i67 expression was found in oral carcinogenesis. The immunolabeling for those markers was higher in OSCC when compared with the other groups (Kruskal-Wallis, p&lt;0.05). Ki-67 expression percentage was higher in OL and in IH when compared with NOM (Kruskal-Wallis/Dunn, p&lt;0.05). Increased expression of BMI-1 was also observed in OL when compared with NOM (Kruskal-Wallis/Dunn, p&lt;0.05). No differences were observed in expression of both markers when non-dysplastic and dysplastic leukoplakias were compared. A significant positive correlation between Ki-67 and BMI-1 was found (Spearman correlation coefficient, R=0.26, p=0.01). High-grade epithelial dysplasia was associated with malignant transformation (Chi-squared, p=0.03). Conclusions These findings indicate that BMI-1 expression increases in early oral carcinogenesis and is possibly associated with the occurrence of dysplastic changes. Furthermore, our findings indicate that both Ki-67 and BMI-1 are directly correlated and play a role in initiation and progression of OSCC.
DOI: 10.6084/m9.figshare.12210830
title: Perillyl alcohol has antibacterial effects and reduces ROS production in macrophages

description: Abstract Natural products have emerged as a rich source of bioactive compounds for adjunctive treatments of many infectious and inflammatory conditions, including periodontitis. Among the monoterpenes with significant biological properties, there is the perillyl alcohol (POH), which can be found in several essential oils and has shown immunomodulatory properties in recent studies, which may be interesting in the treatment of non-neoplastic inflammatory disorders. Objective To determine the antibacterial and immune modulatory activities of the POH. Methodology The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) of the POH for two significant Gram-negative periodontal pathogens were determined by macrodilution and subculture, respectively. Cell proliferation and cytotoxicity in RAW 264.7 macrophages were determined by Trypan Blue and mitochondrial enzymatic activity assay. The modulation of reactive oxygen species (ROS) was analyzed by flow cytometry and expression of TNF and arginase-1 by real-time PCR. Results The POH was effective against P. gingivalis (ATCC 33277) and F. nucleatum (ATCC 25586) with MIC= MBC=1600 μM. No cytotoxicity up to 100 µM was observed on macrophages. The cell proliferation was inhibited from 48 hours at 100 μM (p&lt;0.05) and 250 μM (p&lt;0.01). The POH increased ROS production at both 10 μM and 100 μM (p&lt;0.05) in unstimulated cells. The PMA-induced ROS production was not affected by POH, whereas 100 μM significantly reduced lipopolysaccharide-induced (LPS-induced) ROS. The expression of TNF was not affected by POH in unstimulated cells or in cells polarized to M1 phenotype, whereas both concentrations of POH reduced (p&lt;0.05) the expression of arginase-1 in M2-polarized macrophages. Conclusion The POH has antibacterial activity against periodontal pathogens and reduced proliferation of murine macrophages without significant cytotoxicity at concentrations up to 100 μM. In addition, the POH reduced the LPS-induced ROS and the expression of arginase-1 in M2-polarized macrophages.
DOI: 10.6084/m9.figshare.12210833.v1
title: BMI-1 expression increases in oral leukoplakias and correlates with cell proliferation

description: Abstract Oral leukoplakia (OL) is a white lesion of an indeterminate risk not related to any excluded (other) known diseases or disorders that carry no increased risk for cancer. Many biological markers have been used in an attempt to predict malignant transformation; however, no reliable markers have been established so far. Objective To evaluate cell proliferation and immortalization in OL, comparing non-dysplastic (Non-dys OL) and dysplastic OL (Dys OL). Methodology This is a cross-sectional observational study. Paraffin-embedded tissue blocks of 28 specimens of Non-dys OL, 33 of Dys OL, 9 of normal oral mucosa (NOM), 17 of inflammatory hyperplasia (IH), and 19 of oral squamous cell carcinomas (OSCC) were stained for Ki-67 and BMI-1 using immunohistochemistry. Results A gradual increase in BMI-1 and K-i67 expression was found in oral carcinogenesis. The immunolabeling for those markers was higher in OSCC when compared with the other groups (Kruskal-Wallis, p&lt;0.05). Ki-67 expression percentage was higher in OL and in IH when compared with NOM (Kruskal-Wallis/Dunn, p&lt;0.05). Increased expression of BMI-1 was also observed in OL when compared with NOM (Kruskal-Wallis/Dunn, p&lt;0.05). No differences were observed in expression of both markers when non-dysplastic and dysplastic leukoplakias were compared. A significant positive correlation between Ki-67 and BMI-1 was found (Spearman correlation coefficient, R=0.26, p=0.01). High-grade epithelial dysplasia was associated with malignant transformation (Chi-squared, p=0.03). Conclusions These findings indicate that BMI-1 expression increases in early oral carcinogenesis and is possibly associated with the occurrence of dysplastic changes. Furthermore, our findings indicate that both Ki-67 and BMI-1 are directly correlated and play a role in initiation and progression of OSCC.