cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12850730.v1
title: Measuring maternal body composition by biomedical impedance can predict risk for gestational diabetes mellitus: a retrospective study among 22,223 women

description: This study aimed to identify which element of body composition measurements taken before 17th week gestation was the strongest risk factor for gestational diabetes mellitus (GDM) in Chinese pregnant women. A retrospective study was performed using data retrieved from the Electronic Medical Record database of Chongqing Health Center for Women and Children (China) from January 2014 to December 2015. A total of 22,223 women were included with singleton pregnancies and no preexisting diabetes who underwent bioelectrical impedance analysis (BIA) before 17 gestational weeks and 75-g OGTT at 24–28 gestational weeks. The prevalence of GDM from 2014 to 2015 was 27.13% (IADPSG). All indicators of BIA (total body water, fat mass, fat-free mass, percent body fat, muscle mass, visceral fat levels, proteins, bone minerals, basal metabolic rate, lean trunk mass), age, weight and body mass index (BMI) were risk factors that significantly increased the occurrence of GDM (<i>p</i> &lt; .001 for all). Women older than 30 years or with a BMI more than 23, had a significantly higher GDM prevalence (34.89% and 34.77%). After adjusted covariates, visceral fat levels at the third quartile, the <i>ORs</i> of GDM were 1.142 (95% <i>CI</i> 1.032–1.263) in model I and 1.419 (95% <i>CI</i> 1.274–1.581) in model II used the first quartile as reference (<i>p</i> &lt; .05 for both); bone minerals at the third quartile, the <i>ORs</i> of GDM were 1.124 (95% <i>CI</i> 1.020–1.238) in model I and 1.311 (95% <i>CI</i> 1.192–1.442) in model II (<i>p</i> &lt; .05 for both). After adjusted for age, visceral fat levels and bone minerals, <i>OR</i> of GDM for percent body fat more than 28.77% at the third quartile was 1.334 (95% <i>CI</i> 1.201–1.482) in model II (<i>p</i> &lt; .05 for both). Visceral fat levels, bone minerals and percent body fat were significantly associated with an increased risk of GDM, providing the reference ranges of visceral fat levels, bone minerals and percent body fat as predictive factors for Chinese women to estimate the risk of GDM by BIA during pregnancy.
DOI: 10.6084/m9.figshare.14423605
title: Identification And validation of transcription factor genes involved in prostate cancer metastasis

description: Metastasis is one of the most significant independent risk factors that can negatively affect prostate cancer (PCa) patients. However, the exact mechanisms have not been fully elucidated. To illustrate the mechanisms underlying PCa metastasis, we conducted a series of integrated bioinformatics analyses. The essential genes involved in PCa metastasis were obtained by analyzing differentially expressed genes (DEGs) between metastatic PCa and localized PCa. Gene Ontology and KEGG pathway enrichment analysis were performed for functional annotation. Protein–protein interaction networks were constructed for hub gene selection. Three transcription factor genes (<i>FOS</i>, <i>CENPA</i>, and <i>FOXM1</i>) were identiﬁed by integrating the hub genes with human transcription factors from The Human Transcription Factors database. Moreover, expression validation and prognostic analysis of the three transcription factor genes were carried out on GEO, TCGA, GEPIA, and the Human Protein Atlas, respectively. Further verification showed that expression variation of the three transcription factor genes existed between metastatic PCa and localized PCa as well as between localized PCa and normal prostate. In addition, different expressions of the three transcription factor genes were associated with the prognosis of localized PCa. In summary, the three transcription factor genes can serve as potential prognostic biomarkers as well as therapeutic targets for PCa. <b>Abbreviations:</b> PCa: prostate cancer; DEGs: differentially expressed genes; TFs: transcription factors; GEO: Gene Expression Omnibus; FC: fold change; DAVID: Database for Annotation, Visualization, and Integrated Discovery; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; BP: biological process; CC: cell component; MF: molecular function; PPI: protein–protein interaction; MCODE: Molecular Complex Detection; GEPIA: Gene Expression Profiling Interactive Analysis; GTEx: Genotype-Tissue Expression; TCGA: The Cancer Genome Atlas Program; MCC: Maximal Clique Centrality; DMNC: Density of Maximum Neighborhood Component; MNC: Maximum neighborhood component; EPC: Edge Percolated component; DFS: disease-free survival; OS: overall survival; MAPK: mitogen-activated protein kinases
DOI: 10.6084/m9.figshare.14423605.v1
title: Identification And validation of transcription factor genes involved in prostate cancer metastasis

description: Metastasis is one of the most significant independent risk factors that can negatively affect prostate cancer (PCa) patients. However, the exact mechanisms have not been fully elucidated. To illustrate the mechanisms underlying PCa metastasis, we conducted a series of integrated bioinformatics analyses. The essential genes involved in PCa metastasis were obtained by analyzing differentially expressed genes (DEGs) between metastatic PCa and localized PCa. Gene Ontology and KEGG pathway enrichment analysis were performed for functional annotation. Protein–protein interaction networks were constructed for hub gene selection. Three transcription factor genes (<i>FOS</i>, <i>CENPA</i>, and <i>FOXM1</i>) were identiﬁed by integrating the hub genes with human transcription factors from The Human Transcription Factors database. Moreover, expression validation and prognostic analysis of the three transcription factor genes were carried out on GEO, TCGA, GEPIA, and the Human Protein Atlas, respectively. Further verification showed that expression variation of the three transcription factor genes existed between metastatic PCa and localized PCa as well as between localized PCa and normal prostate. In addition, different expressions of the three transcription factor genes were associated with the prognosis of localized PCa. In summary, the three transcription factor genes can serve as potential prognostic biomarkers as well as therapeutic targets for PCa. <b>Abbreviations:</b> PCa: prostate cancer; DEGs: differentially expressed genes; TFs: transcription factors; GEO: Gene Expression Omnibus; FC: fold change; DAVID: Database for Annotation, Visualization, and Integrated Discovery; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; BP: biological process; CC: cell component; MF: molecular function; PPI: protein–protein interaction; MCODE: Molecular Complex Detection; GEPIA: Gene Expression Profiling Interactive Analysis; GTEx: Genotype-Tissue Expression; TCGA: The Cancer Genome Atlas Program; MCC: Maximal Clique Centrality; DMNC: Density of Maximum Neighborhood Component; MNC: Maximum neighborhood component; EPC: Edge Percolated component; DFS: disease-free survival; OS: overall survival; MAPK: mitogen-activated protein kinases
DOI: 10.6084/m9.figshare.7607897
title: Additional file 1: of Potential gains in health-adjusted life expectancy from reducing four main non-communicable diseases among Chinese elderly

description: GBD cause list. This additional file 1 included the details of the GBD cause list. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7607897.v1
title: Additional file 1: of Potential gains in health-adjusted life expectancy from reducing four main non-communicable diseases among Chinese elderly

description: GBD cause list. This additional file 1 included the details of the GBD cause list. (XLSX 25 kb)
DOI: 10.5281/zenodo.10663930
title: CIMURA_10krun
DOI: 10.5281/zenodo.10663931
title: CIMURA_10krun
DOI: 10.6084/m9.figshare.7607939
title: Additional file 1: of High admission rates and heavy inpatient service costs of urban tuberculosis patients in eastern China

description: Details of the 356â TB patients. These data contain demographic and social characteristics of the 356â TB patients, including gender, age, occupation, patient category, residence, sputum smear test, hospitalization status, type of health insurance, etc. (XLS 70 kb)
DOI: 10.6084/m9.figshare.7607939.v1
title: Additional file 1: of High admission rates and heavy inpatient service costs of urban tuberculosis patients in eastern China

description: Details of the 356â TB patients. These data contain demographic and social characteristics of the 356â TB patients, including gender, age, occupation, patient category, residence, sputum smear test, hospitalization status, type of health insurance, etc. (XLS 70 kb)
DOI: 10.6084/m9.figshare.7607945
title: Additional file 2: of High admission rates and heavy inpatient service costs of urban tuberculosis patients in eastern China

description: Details of the 221â TB inpatients. These data contain the hospitalization records of 221 inpatients, including hospitalization times, length of hospital stay, and type of health insurance. (XLS 48 kb)
DOI: 10.6084/m9.figshare.7607945.v1
title: Additional file 2: of High admission rates and heavy inpatient service costs of urban tuberculosis patients in eastern China

description: Details of the 221â TB inpatients. These data contain the hospitalization records of 221 inpatients, including hospitalization times, length of hospital stay, and type of health insurance. (XLS 48 kb)
DOI: 10.6084/m9.figshare.23968884
title: Dataset of Flow and Transport in Rock Fracture from DNS, Inverse Modelling, and Direct Prediction

description: This dataset comprises flow and transport-related data for 20 fracture models at various Reynolds numbers, including pressure-flow curves, solute breakthrough curves, residence time distributions, and results of transport coefficient correlation analyses along with their parameterized characterizations.
DOI: 10.6084/m9.figshare.7607954
title: Additional file 3: of High admission rates and heavy inpatient service costs of urban tuberculosis patients in eastern China

description: Medical expenditure of the 141 inpatients. These data contain the social characteristics and hospitalization expenditures of 141â TB inpatients, including total costs and OOP costs. (XLS 44 kb)
DOI: 10.6084/m9.figshare.7607954.v1
title: Additional file 3: of High admission rates and heavy inpatient service costs of urban tuberculosis patients in eastern China

description: Medical expenditure of the 141 inpatients. These data contain the social characteristics and hospitalization expenditures of 141â TB inpatients, including total costs and OOP costs. (XLS 44 kb)
DOI: 10.6084/m9.figshare.12850895
title: A preliminary study of atypical cortical change ability of dynamic whole-brain functional connectivity in autism spectrum disorder

description: Designing new objectively diagnostic methods of autism spectrum disorder (ASD) are burning questions. Dynamic functional connectivity (DFC) methodology based on fMRI data are an effective lever to investigate changeability evolution of signal synchronization in macroscopic neural activity patterns. Embracing the network dynamics concepts, this paper introduces changeability index (C-score)which is focused on time-varying aspects of FCs, and develops a new framework for researching the roots of ASD brains at resting states in holism significance. The important process is to uncover noticeable regions and subsystems endowed with antagonistic stance in C-scores of between atypical and typical DFCs of 30 healthy controls (HCs) and 48 ASD patients. The abnormities of edge C-scores are found across widespread brain cortex in ASD brains. For whole brain regional C-scores of ASD patients, orbitofrontal middle cortex L, inferior triangular frontal gyrus L, middle occipital gyrus L, postcentral gyrus L, supramarginal L, supramarginal R, cerebellum 8 L, and cerebellum 10 Rare endowed with significantly different C-scores.At brain subsystems level, C-scores in left hemisphere, right hemisphere, top hemisphere, bottom hemisphere, frontal lobe, parietal lobe, occipital lobe, cerebellum sub systems are abnormal in ASD patients. The ASD brains have whole-brain abnormity on widespread regions. Through the strict evidence-based study, it was found that the changeability index (C-score) is a meaningful biological marker to explore cortical activity in ASD.
DOI: 10.6084/m9.figshare.12850895.v1
title: A preliminary study of atypical cortical change ability of dynamic whole-brain functional connectivity in autism spectrum disorder

description: Designing new objectively diagnostic methods of autism spectrum disorder (ASD) are burning questions. Dynamic functional connectivity (DFC) methodology based on fMRI data are an effective lever to investigate changeability evolution of signal synchronization in macroscopic neural activity patterns. Embracing the network dynamics concepts, this paper introduces changeability index (C-score)which is focused on time-varying aspects of FCs, and develops a new framework for researching the roots of ASD brains at resting states in holism significance. The important process is to uncover noticeable regions and subsystems endowed with antagonistic stance in C-scores of between atypical and typical DFCs of 30 healthy controls (HCs) and 48 ASD patients. The abnormities of edge C-scores are found across widespread brain cortex in ASD brains. For whole brain regional C-scores of ASD patients, orbitofrontal middle cortex L, inferior triangular frontal gyrus L, middle occipital gyrus L, postcentral gyrus L, supramarginal L, supramarginal R, cerebellum 8 L, and cerebellum 10 Rare endowed with significantly different C-scores.At brain subsystems level, C-scores in left hemisphere, right hemisphere, top hemisphere, bottom hemisphere, frontal lobe, parietal lobe, occipital lobe, cerebellum sub systems are abnormal in ASD patients. The ASD brains have whole-brain abnormity on widespread regions. Through the strict evidence-based study, it was found that the changeability index (C-score) is a meaningful biological marker to explore cortical activity in ASD.
DOI: 10.6084/m9.figshare.12850904
title: Tuberculosis relapse is more common than reinfection in Beijing, China

description: Recurrent tuberculosis (TB) is a major health problem in countries with a high TB burden. It is very necessary to elucidate the situation of recurrent TB in Beijing, capital of China. To determine the proportion of recurrent tuberculosis (TB) cases and to identify relapsed or reinfected cases, as well as risk factors associated with recurrence in Beijing. We conducted a retrospective study that included all TB cases in Beijing that were successfully treated from 2013 to 2015. Recurrence due to relapse or reinfection was determined using the variable number of tandem repeats (VNTR) method. Risk factors associated with recurrence were analysed. Tuberculosis recurred in 275 of the 4043 successfully treated TB patients, giving a recurrence rate of 6.8% (275/4043). 190 of the 275 cases were culture positive in both instances, and genotyping results for both episodes were available for 58 of these patients. The cultured isolates from 40 of the 58 recurrent cases (69%) had identical genotypic patterns in both episodes, indicating a relapse. 31% (18/58) had different genotypes, indicating reinfection by a new strain and suggested recent transmission. Those people in the 30–59 age group (<i>p</i> &lt; .001), and those retreated for pulmonary TB (<i>p</i> &lt; .001) were more likely to have TB recurrence. Our results indicate that relapse was more common than reinfection in recurrent TB cases in Beijing from 2013 to 2015. Age and retreatment were found to be risk factors for TB recurrence.
DOI: 10.6084/m9.figshare.12850904.v1
title: Tuberculosis relapse is more common than reinfection in Beijing, China

description: Recurrent tuberculosis (TB) is a major health problem in countries with a high TB burden. It is very necessary to elucidate the situation of recurrent TB in Beijing, capital of China. To determine the proportion of recurrent tuberculosis (TB) cases and to identify relapsed or reinfected cases, as well as risk factors associated with recurrence in Beijing. We conducted a retrospective study that included all TB cases in Beijing that were successfully treated from 2013 to 2015. Recurrence due to relapse or reinfection was determined using the variable number of tandem repeats (VNTR) method. Risk factors associated with recurrence were analysed. Tuberculosis recurred in 275 of the 4043 successfully treated TB patients, giving a recurrence rate of 6.8% (275/4043). 190 of the 275 cases were culture positive in both instances, and genotyping results for both episodes were available for 58 of these patients. The cultured isolates from 40 of the 58 recurrent cases (69%) had identical genotypic patterns in both episodes, indicating a relapse. 31% (18/58) had different genotypes, indicating reinfection by a new strain and suggested recent transmission. Those people in the 30–59 age group (<i>p</i> &lt; .001), and those retreated for pulmonary TB (<i>p</i> &lt; .001) were more likely to have TB recurrence. Our results indicate that relapse was more common than reinfection in recurrent TB cases in Beijing from 2013 to 2015. Age and retreatment were found to be risk factors for TB recurrence.
DOI: 10.6084/m9.figshare.19142363
title: Bioinformatics analysis deciphering the transcriptomic signatures associated with signalling pathways and prognosis in the myelodysplastic syndromes

description: Background: Several studies scatteredly identified the myelodysplastic syndromes’ transcriptomic profiles (MDS). However, the exploration of transcriptional signatures, key signalling pathways, and their association with prognosis and diagnosis in the integrated multiple datasets remains lacking. Methods: We integrated the GSE4619, GSE19429, GSE30195, and GSE58831 microarray datasets of CD34 + cells for identifying the differentially expressed genes (DEGs) in the MDS. The series of bioinformatics methods are applied to identify the key hub genes, gene clusters, prognostic hub genes, and genes associated with diagnostic efficacy. Finally, we validated the expression differences of hub genes in the GSE114922 dataset. Results: We explored the DEGs related to gene ontology enrichment and KEGG pathways. We identified significant hub genes, including 168 upregulated hub genes (such as <i>STAT1, IFIH1, EPRS, GRB2, RAC2, MAPK14, CASP1, and SPI1</i>) and 52 downregulated hub genes (such as <i>CREBBP, HIF1A, PIK3CA, EZH2, PIK3R1, MDM2, IRF4, CXCR4, PCNA,</i> and <i>CD19</i>) in the MDS. In addition, we identified six significant molecular complex detection (MCODE)-derived upregulated gene clusters and one downregulated gene cluster, respectively. Moreover, we found that the higher expression level of <i>MX2, GBP2, PXN, IFI44, FDXR, PLCB2, ASS1, ERCC4, PML,</i> and <i>RRAGD</i> and the lower expression level of <i>CD19, PAX5, TCF3, LEF1, NUSAP1,</i> and <i>TIMELESS</i> hub genes are significantly correlated with shorter survival times of MDS patients. Furthermore, the area value under the ROC curve (AUC) of <i>PXN, FDXR, PLCB2, PML, CD19, PAX5,</i> and <i>LEF1</i> prognostic genes are more than 0.80, indicating that these genes could be effectively used for the diagnostic efficacy of MDS patients. Conclusions: Identifying key hub genes and their association with the prognosis and diagnostic efficacy may provide substantial clues for the treatment and diagnosis of MDS patients.
DOI: 10.6084/m9.figshare.19142363.v1
title: Bioinformatics analysis deciphering the transcriptomic signatures associated with signalling pathways and prognosis in the myelodysplastic syndromes

description: Background: Several studies scatteredly identified the myelodysplastic syndromes’ transcriptomic profiles (MDS). However, the exploration of transcriptional signatures, key signalling pathways, and their association with prognosis and diagnosis in the integrated multiple datasets remains lacking. Methods: We integrated the GSE4619, GSE19429, GSE30195, and GSE58831 microarray datasets of CD34 + cells for identifying the differentially expressed genes (DEGs) in the MDS. The series of bioinformatics methods are applied to identify the key hub genes, gene clusters, prognostic hub genes, and genes associated with diagnostic efficacy. Finally, we validated the expression differences of hub genes in the GSE114922 dataset. Results: We explored the DEGs related to gene ontology enrichment and KEGG pathways. We identified significant hub genes, including 168 upregulated hub genes (such as <i>STAT1, IFIH1, EPRS, GRB2, RAC2, MAPK14, CASP1, and SPI1</i>) and 52 downregulated hub genes (such as <i>CREBBP, HIF1A, PIK3CA, EZH2, PIK3R1, MDM2, IRF4, CXCR4, PCNA,</i> and <i>CD19</i>) in the MDS. In addition, we identified six significant molecular complex detection (MCODE)-derived upregulated gene clusters and one downregulated gene cluster, respectively. Moreover, we found that the higher expression level of <i>MX2, GBP2, PXN, IFI44, FDXR, PLCB2, ASS1, ERCC4, PML,</i> and <i>RRAGD</i> and the lower expression level of <i>CD19, PAX5, TCF3, LEF1, NUSAP1,</i> and <i>TIMELESS</i> hub genes are significantly correlated with shorter survival times of MDS patients. Furthermore, the area value under the ROC curve (AUC) of <i>PXN, FDXR, PLCB2, PML, CD19, PAX5,</i> and <i>LEF1</i> prognostic genes are more than 0.80, indicating that these genes could be effectively used for the diagnostic efficacy of MDS patients. Conclusions: Identifying key hub genes and their association with the prognosis and diagnostic efficacy may provide substantial clues for the treatment and diagnosis of MDS patients.
DOI: 10.6084/m9.figshare.7608032
title: Additional file 2: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

description: Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list of the 300 top-ranked genes for each tool. (XLSX 115â kb)
DOI: 10.6084/m9.figshare.7608032.v1
title: Additional file 2: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

description: Results of the Gene Ontology Process enrichment analysis of the 300 top-ranked DE genes and the list of the 300 top-ranked genes for each tool. (XLSX 115â kb)
DOI: 10.6084/m9.figshare.7608038
title: Additional file 3: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

description: Significant GO terms with their negative log transform of their q-values for each tool. (CSV 24â kb)
DOI: 10.6084/m9.figshare.7608038.v1
title: Additional file 3: of Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

description: Significant GO terms with their negative log transform of their q-values for each tool. (CSV 24â kb)
DOI: 10.6084/m9.figshare.12850937
title: Comparison of Intraocular Antibody Measurement, Quantitative Pathogen PCR, and Metagenomic Deep Sequencing of Aqueous Humor in Secondary Glaucoma Associated with Anterior Segment Uveitis

description: To identify viral pathogens in patients with secondary glaucoma associated with anterior segment uveitis and compare metagenomic deep sequencing (MDS) with enzyme-linked immunosorbent assay (ELISA) combined with Witmer-Desmonts coefficient (WDC) evaluation and real-time quantitative polymerase chain reaction (qPCR) on investigating pathogens in aqueous humor. Aqueous humor from 31 patients, including 22 Posner-Schlossman Syndrome and 9 other anterior uveitis, was assessed pathogens by ELISA combined with WDC evaluation, virus deoxyribonucleic acid (DNA) detection by real-time qPCR and MDS. Viral pathogens (HCMV or VZV or RV) were detected in 19 out of 31 eyes (61.3%) by real-time qPCR or WDC evaluation. MDS revealed the presence of HCMV DNA sequences in three PSS patients. Virus is an important pathogen in secondary glaucoma associated with anterior segment uveitis. MDS is a potential etiologic diagnosis tool to seek intraocular viral pathogens for secondary glaucoma associated anterior segment uveitis.