cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11376849
title: MOESM3 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 3: Table S3. 615 Brucella strains (B. suis and B. canis) were used to construct the MST on a global scale (strains in this study are indicated with yellow circles).
DOI: 10.6084/m9.figshare.11376855
title: MOESM4 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 4: Table S4. Table representing isolates key, allele characters, ST, species, host, and year of collection of strains were used for MLST analysis.
DOI: 10.6084/m9.figshare.11376801.v1
title: MOESM1 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 1: Table S1. Table representing strain identification codes (Key), MLVA-8 data, MLVA-11 data, biovars, and year of isolation for 40 Brucella isolates.
DOI: 10.6084/m9.figshare.11376879
title: MOESM2 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 2: Table S2. COG function annotation of Shewanella sp. MR-7.
DOI: 10.6084/m9.figshare.11376924
title: MOESM7 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 7: Table S7. The relative abundance of intestinal bacterial OTUs at genus taxonomic levels.
DOI: 10.6084/m9.figshare.12949534
title: Additional file 7 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 7. Information on taxonomic annotation of co-abundant gene clusters (CAG). For each CAG, the bacterial species contributing the highest–and second highest–number of genes is shown. For the most contributing species, the percentage of genes assigned to that species is shown in “PercentageOfTaxonContribution”. The column “trusted” indicates if the corresponding cluster passed our annotation criteria.
DOI: 10.6084/m9.figshare.12949534.v1
title: Additional file 7 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 7. Information on taxonomic annotation of co-abundant gene clusters (CAG). For each CAG, the bacterial species contributing the highest–and second highest–number of genes is shown. For the most contributing species, the percentage of genes assigned to that species is shown in “PercentageOfTaxonContribution”. The column “trusted” indicates if the corresponding cluster passed our annotation criteria.
DOI: 10.6084/m9.figshare.11376819
title: MOESM2 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 2: Table S2. 340 Chinese Brucella strains were used to construct the MST (strains in this study are indicated with yellow circles).
DOI: 10.6084/m9.figshare.12949528
title: Additional file 5 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 5. Growth rate indices of bacterial strains per sample as estimated by GRiD. GRiD values of 1 imply no growth.
DOI: 10.6084/m9.figshare.12949540
title: Additional file 9 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 9. MGS network properties and statistical results for differences in node degree between time points.
DOI: 10.6084/m9.figshare.12949623
title: <i>CYP2S1</i> might regulate proliferation and immune response of keratinocyte in psoriasis

description: Psoriasis is an autoimmune skin disorder influenced by genetic, epigenetic and environmental factors. We previously found <i>CYP2S1</i> intragenic DNA methylation cg19430423 site strongly hypomethylated in psoriatic skin tissues. In this study, we performed methylation loci fine-mapping to search the top signals in the entire <i>CYP2S1</i> gene region, and further carried out gene expression assay, cell proliferation, apoptosis, differentiation and migration in <i>CYP2S1</i> overexpressed (<i>CYP2S1</i><sup>over</sup>) and silenced (siRNA) human keratinocytes. Target bisulphite conversion sequencing revealed cg19430423 and nearby two loci were the top differentially methylated loci. These three loci located within active enhancer region marked by H3K4Me1 and H3K27AC peaks. Cg19430423 might not bind with ATF1 directly. <i>CYP2S1</i><sup>over</sup> repressed NHEK cell proliferation, but have no confirmed evidence on affecting migration, apoptosis and differentiation. Real-time PCR showed that <i>CYP2S1</i> inhibited expression of <i>IL1β, IL8, IL33, IL36, LL37, CXCL10</i> and <i>CCL20</i> gene. In summary, <i>CYP2S1</i> might inhibit keratinocyte proliferation, and modulate immune response through <i>IL-8, IL-33, IL-36, CXCL-10, CCL20</i>, thus contribute to the development of psoriasis.
DOI: 10.6084/m9.figshare.11376900
title: MOESM4 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 4: Table S4. Genes involved in fatty acid metabolism in the genome of Shewanella sp. MR-7.
DOI: 10.6084/m9.figshare.12949623.v1
title: <i>CYP2S1</i> might regulate proliferation and immune response of keratinocyte in psoriasis

description: Psoriasis is an autoimmune skin disorder influenced by genetic, epigenetic and environmental factors. We previously found <i>CYP2S1</i> intragenic DNA methylation cg19430423 site strongly hypomethylated in psoriatic skin tissues. In this study, we performed methylation loci fine-mapping to search the top signals in the entire <i>CYP2S1</i> gene region, and further carried out gene expression assay, cell proliferation, apoptosis, differentiation and migration in <i>CYP2S1</i> overexpressed (<i>CYP2S1</i><sup>over</sup>) and silenced (siRNA) human keratinocytes. Target bisulphite conversion sequencing revealed cg19430423 and nearby two loci were the top differentially methylated loci. These three loci located within active enhancer region marked by H3K4Me1 and H3K27AC peaks. Cg19430423 might not bind with ATF1 directly. <i>CYP2S1</i><sup>over</sup> repressed NHEK cell proliferation, but have no confirmed evidence on affecting migration, apoptosis and differentiation. Real-time PCR showed that <i>CYP2S1</i> inhibited expression of <i>IL1β, IL8, IL33, IL36, LL37, CXCL10</i> and <i>CCL20</i> gene. In summary, <i>CYP2S1</i> might inhibit keratinocyte proliferation, and modulate immune response through <i>IL-8, IL-33, IL-36, CXCL-10, CCL20</i>, thus contribute to the development of psoriasis.
DOI: 10.6084/m9.figshare.16619738.v1
title: Fitting Multilevel Vector Autoregressive Models in Stan, JAGS, and Mplus

description: The influx of intensive longitudinal data creates a pressing need for complex modeling tools that help enrich our understanding of how individuals change over time. Multilevel vector autoregressive (mlVAR) models allow for simultaneous evaluations of reciprocal linkages between dynamic processes and individual differences, and have gained increased recognition in recent years. High-dimensional and other complex variations of mlVAR models, though often computationally intractable in the frequentist framework, can be readily handled using Markov chain Monte Carlo techniques in a Bayesian framework. However, researchers in social science fields may be unfamiliar with ways to capitalize on recent developments in Bayesian software programs. In this paper, we provide step-by-step illustrations and comparisons of options to fit Bayesian mlVAR models using Stan, JAGS and Mplus, supplemented with a Monte Carlo simulation study. An empirical example is used to demonstrate the utility of mlVAR models in studying intra- and inter-individual variations in affective dynamics.
DOI: 10.6084/m9.figshare.11376867
title: MOESM2 of Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer’s disease-related dysregulation

description: Additional file 2: Table S1. CpGs DS vs Ctrl. Table S2. DMR DS vs Ctrl. Table S3. This table is adapted from a gene list presented in Fig. 3c by Do et al. (2017). Table S4. DMR IQ- vs IQ+.
DOI: 10.6084/m9.figshare.11376864
title: MOESM5 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 5: Table S5. Isolates from Guangxi province had identical MLVA-16 genotypes with strains from other provinces of China.
DOI: 10.6084/m9.figshare.16619738.v2
title: Fitting Multilevel Vector Autoregressive Models in Stan, JAGS, and Mplus

description: The influx of intensive longitudinal data creates a pressing need for complex modeling tools that help enrich our understanding of how individuals change over time. Multilevel vector autoregressive (mlVAR) models allow for simultaneous evaluations of reciprocal linkages between dynamic processes and individual differences, and have gained increased recognition in recent years. High-dimensional and other complex variations of mlVAR models, though often computationally intractable in the frequentist framework, can be readily handled using Markov chain Monte Carlo techniques in a Bayesian framework. However, researchers in social science fields may be unfamiliar with ways to capitalize on recent developments in Bayesian software programs. In this paper, we provide step-by-step illustrations and comparisons of options to fit Bayesian mlVAR models using Stan, JAGS and Mplus, supplemented with a Monte Carlo simulation study. An empirical example is used to demonstrate the utility of mlVAR models in studying intra- and inter-individual variations in affective dynamics.
DOI: 10.6084/m9.figshare.11376849.v1
title: MOESM3 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 3: Table S3. 615 Brucella strains (B. suis and B. canis) were used to construct the MST on a global scale (strains in this study are indicated with yellow circles).
DOI: 10.6084/m9.figshare.11376918
title: MOESM6 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 6: Table S6. The relative abundance of intestinal bacterial OTUs at phylum taxonomic levels.
DOI: 10.6084/m9.figshare.11376924.v1
title: MOESM7 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 7: Table S7. The relative abundance of intestinal bacterial OTUs at genus taxonomic levels.
DOI: 10.6084/m9.figshare.12949495
title: Additional file 11 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 11. List of bacterial species with predicted positive or negative correlation to selected fungal species. The table further contains information on the corresponding MGS, time-related fold-changes, and for which antibiotic drugs the observation was made.
DOI: 10.6084/m9.figshare.11376864.v1
title: MOESM5 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 5: Table S5. Isolates from Guangxi province had identical MLVA-16 genotypes with strains from other provinces of China.
DOI: 10.6084/m9.figshare.11376894
title: MOESM3 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 3: Table S3. KEGG pathway of Shewanella sp. MR-7.
DOI: 10.6084/m9.figshare.11376855.v1
title: MOESM4 of Investigation of the molecular characteristics of Brucella isolates from Guangxi Province, China

description: Additional file 4: Table S4. Table representing isolates key, allele characters, ST, species, host, and year of collection of strains were used for MLST analysis.
DOI: 10.6084/m9.figshare.11376894.v1
title: MOESM3 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 3: Table S3. KEGG pathway of Shewanella sp. MR-7.
DOI: 10.6084/m9.figshare.11376900.v1
title: MOESM4 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 4: Table S4. Genes involved in fatty acid metabolism in the genome of Shewanella sp. MR-7.
DOI: 10.6084/m9.figshare.12949492.v1
title: Additional file 10 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 10. Cross-kingdom correlations representing the MGS-ITS correlation network. Correlations are listed for each time point.
DOI: 10.6084/m9.figshare.11376879.v1
title: MOESM2 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 2: Table S2. COG function annotation of Shewanella sp. MR-7.
DOI: 10.6084/m9.figshare.11376918.v1
title: MOESM6 of Improved utilization of soybean meal through fermentation with commensal Shewanella sp. MR-7 in turbot (Scophthalmus maximus L.)

description: Additional file 6: Table S6. The relative abundance of intestinal bacterial OTUs at phylum taxonomic levels.
DOI: 10.6084/m9.figshare.12949634.v3
title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study

description: The cause of some patients with negative RT-PCR results experienced turn-positive after treatment remains unclear. In addition, understanding the correlation between changes in clinical data in the course of COVID-19 and treatment outcomes is of great importance in determining the prognosis of COVID-19. To perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. Clinical data, including clinical manifestations, laboratory tests, radiography results, treatment methods and outcomes, were retrospectively collected and analyzed from January to March 2020 in Renmin Hospitals of Wuhan University. 116 COVID-19 patients (40 in recurrent group, 29 in recovered group and 47 in unrecovered group) were recruited. In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. CD19 and CT scan results were found notable difference between recurrent group and recovered group. Odds from CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT scan results validated associations with clinical outcomes of COVID-19. The so-called recurrence in some COVID-19 patients may be due to the false-negative of nucleic acid test results from nasopharyngeal swabs. Levels of CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT results were significantly correlated with the outcome of COVID-19. The cellular immunity test could be beneficial to further screen the reliability of RT-PCR test on the basis of CT images.
DOI: 10.6084/m9.figshare.12949634.v2
title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study

description: The cause of some patients with negative RT-PCR results experienced turn-positive after treatment remains unclear. In addition, understanding the correlation between changes in clinical data in the course of COVID-19 and treatment outcomes is of great importance in determining the prognosis of COVID-19. To perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. Clinical data, including clinical manifestations, laboratory tests, radiography results, treatment methods and outcomes, were retrospectively collected and analyzed from January to March 2020 in Renmin Hospitals of Wuhan University. 116 COVID-19 patients (40 in recurrent group, 29 in recovered group and 47 in unrecovered group) were recruited. In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. CD19 and CT scan results were found notable difference between recurrent group and recovered group. Odds from CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT scan results validated associations with clinical outcomes of COVID-19. The so-called recurrence in some COVID-19 patients may be due to the false-negative of nucleic acid test results from nasopharyngeal swabs. Levels of CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT results were significantly correlated with the outcome of COVID-19. The cellular immunity test could be beneficial to further screen the reliability of RT-PCR test on the basis of CT images.
DOI: 10.6084/m9.figshare.11376867.v1
title: MOESM2 of Methylomic profiling in trisomy 21 identifies cognition- and Alzheimer’s disease-related dysregulation

description: Additional file 2: Table S1. CpGs DS vs Ctrl. Table S2. DMR DS vs Ctrl. Table S3. This table is adapted from a gene list presented in Fig. 3c by Do et al. (2017). Table S4. DMR IQ- vs IQ+.
DOI: 10.6084/m9.figshare.12949634
title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study

description: The cause of some patients with negative RT-PCR results experienced turn-positive after treatment remains unclear. In addition, understanding the correlation between changes in clinical data in the course of COVID-19 and treatment outcomes is of great importance in determining the prognosis of COVID-19. To perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. Clinical data, including clinical manifestations, laboratory tests, radiography results, treatment methods and outcomes, were retrospectively collected and analyzed from January to March 2020 in Renmin Hospitals of Wuhan University. 116 COVID-19 patients (40 in recurrent group, 29 in recovered group and 47 in unrecovered group) were recruited. In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. CD19 and CT scan results were found notable difference between recurrent group and recovered group. Odds from CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT scan results validated associations with clinical outcomes of COVID-19. The so-called recurrence in some COVID-19 patients may be due to the false-negative of nucleic acid test results from nasopharyngeal swabs. Levels of CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT results were significantly correlated with the outcome of COVID-19. The cellular immunity test could be beneficial to further screen the reliability of RT-PCR test on the basis of CT images.
DOI: 10.6084/m9.figshare.12949639
title: Hypervirulent <i>Klebsiella pneumoniae</i> is emerging as an increasingly prevalent <i>K. pneumoniae</i> pathotype responsible for nosocomial and healthcare-associated infections in Beijing, China

description: Hypervirulent Klebsiella pneumoniae(hvKp) is an increasingly important pathogen. Tracking its epidemiology and evolving antimicrobial resistance will facilitate care. A retrospective study was conducted in two hospitals. We collected the clinical data. Antimicrobial and virulence-associated phenotype and genotype, sequence type, and whole genome sequencing of selected strains were performed. HvKp was defined by the presence of some combination of <sub>p</sub>rmpA, <sub>p</sub>rmpA2, iucA, iroB, and peg-344, genes shown to accurately identify hvKp. Of 158 Kp clinical isolates, 79 (50%) were hvKp. Interestingly, 53/79 (67.1%) of hvKp strains were isolated from patients with nosocomial infection and 19/79 (24.1%) from patients with healthcare-associated infection, but only 7/79 (8.8%) from patients with community-acquired infections. Importantly, 27/53 (50.9%) and 4/19 (21.1%) of hvKp nosocomial and healthcare-associated isolates, respectively, were multi-drug-resistant (MDR); 25/53 (47.2%) and 5/19 (26.3%) expressed ESBLs and 14/53 (26.4%) and 2/19 (10.5%) were carbapenem-resistant. Of the hvKp isolates from community-acquired infection, 0/7 (0%) were MDR and 0/7 (0%) were carbapenem-resistant. Additionally, unique characteristics of nosocomial, healthcare-associated, and community-acquired hvKp infection were identified. In summary, 50% of K. pneumoniae infections were caused by hvKp. A concerning, novel finding from this report is a major shift in hvKp epidemiology. Ninety-one percent of hvKp infections were nosocomial or healthcare-associated, and 43.1% of these isolates were MDR. These data suggest that hvKp may be replacing classical K. pneumoniae as the dominant nosocomial and healthcare-associated pathotype. Ongoing surveillance is needed to determine if this trend is occurring elsewhere.
DOI: 10.6084/m9.figshare.12949501
title: Additional file 13 of Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

description: Additional file 13. Significant correlations between fungal species and stool metabolites.
DOI: 10.6084/m9.figshare.12949634.v1
title: Exploration of turn-positive RT-PCR results and factors related to treatment outcome in COVID-19: A retrospective cohort study

description: The cause of some patients with negative RT-PCR results experienced turn-positive after treatment remains unclear. In addition, understanding the correlation between changes in clinical data in the course of COVID-19 and treatment outcomes is of great importance in determining the prognosis of COVID-19. To perform cause analysis of RT-PCR turn-positive and the effective screening factors related to treatment outcome in COVID-19. Clinical data, including clinical manifestations, laboratory tests, radiography results, treatment methods and outcomes, were retrospectively collected and analyzed from January to March 2020 in Renmin Hospitals of Wuhan University. 116 COVID-19 patients (40 in recurrent group, 29 in recovered group and 47 in unrecovered group) were recruited. In the recurrent group, white blood cell, Neutrophils, prothrombin time, activated partial thromboplastin time, CD3, CD4, CD8, ratio of CD4/CD8, IgG and C4 complement were of significant difference among the baseline, negative and turn-positive time points. CD19 and CT scan results were found notable difference between recurrent group and recovered group. Odds from CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT scan results validated associations with clinical outcomes of COVID-19. The so-called recurrence in some COVID-19 patients may be due to the false-negative of nucleic acid test results from nasopharyngeal swabs. Levels of CD3, CD4, CD8, CD19, IgM, C3 complement, C4 complement and CT results were significantly correlated with the outcome of COVID-19. The cellular immunity test could be beneficial to further screen the reliability of RT-PCR test on the basis of CT images.