cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13177234.v3
title: An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics

description: Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4<sup>+</sup> and CD8<sup>+</sup> T cells and interferon-responsive CD8<sup>+</sup> T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8<sup>+</sup> T cell population expressing KLRG1, TIGIT, and T-bet<sup>dim</sup>Eomes<sup>hi</sup> markers. <i>Ex-vivo</i> antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8<sup>+</sup> T cells demonstrating the contribution of KLRG1<sup>+</sup> population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
DOI: 10.6084/m9.figshare.22614311.v1
title: Additional file 4 of Calcium-to-phosphorus releasing ratio affects osteoinductivity and osteoconductivity of calcium phosphate bioceramics in bone tissue engineering

description: Additional file 4: Table S4. SM Hit Listing of β-TCP sample.
DOI: 10.6084/m9.figshare.13177234.v1
title: An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics

description: Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4<sup>+</sup> and CD8<sup>+</sup> T cells and interferon-responsive CD8<sup>+</sup> T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8<sup>+</sup> T cell population expressing KLRG1, TIGIT, and T-bet<sup>dim</sup>Eomes<sup>hi</sup> markers. <i>Ex-vivo</i> antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8<sup>+</sup> T cells demonstrating the contribution of KLRG1<sup>+</sup> population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
DOI: 10.6084/m9.figshare.13177234
title: An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics

description: Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4<sup>+</sup> and CD8<sup>+</sup> T cells and interferon-responsive CD8<sup>+</sup> T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8<sup>+</sup> T cell population expressing KLRG1, TIGIT, and T-bet<sup>dim</sup>Eomes<sup>hi</sup> markers. <i>Ex-vivo</i> antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8<sup>+</sup> T cells demonstrating the contribution of KLRG1<sup>+</sup> population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
DOI: 10.6084/m9.figshare.13177234.v2
title: An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics

description: Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4<sup>+</sup> and CD8<sup>+</sup> T cells and interferon-responsive CD8<sup>+</sup> T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8<sup>+</sup> T cell population expressing KLRG1, TIGIT, and T-bet<sup>dim</sup>Eomes<sup>hi</sup> markers. <i>Ex-vivo</i> antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8<sup>+</sup> T cells demonstrating the contribution of KLRG1<sup>+</sup> population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.
DOI: 10.6084/m9.figshare.6885956.v1
title: Additional file 1: of Maternal central obesity and birth size: a Mendelian randomization analysis

description: Table S1a. WHRadjBMI loci achieving genome-wide significance (P &lt; 5 × 10–8) in European women-specific meta-analyses. Table S1b. WCadjBMI loci achieving genome-wide significance (P &lt; 5 × 10–8) in European women-specific meta-analyses. Table S1c. HIPadjBMI loci achieving genome-wide significance (P &lt; 5 × 10–8) in European women-specific meta-analyses. (XLSX 22 kb)
DOI: 10.5281/zenodo.10631307
title: Dataset related to article: A DISCRIMINATIVE EVENT-BASED MODEL FOR SUBTYPE DIAGNOSIS OF SPORADIC CREUTZFELDT-JAKOB DISEASE USING BRAIN MRI

description: The database include the raw data about age, sex, sCJD subtype and disease duration of the patients included in the study.
DOI: 10.5281/zenodo.10631308
title: Dataset related to article: A DISCRIMINATIVE EVENT-BASED MODEL FOR SUBTYPE DIAGNOSIS OF SPORADIC CREUTZFELDT-JAKOB DISEASE USING BRAIN MRI

description: The database include the raw data about age, sex, sCJD subtype and disease duration of the patients included in the study.
DOI: 10.6084/m9.figshare.12128820.v1
title: Supplementary material-Raw data for RMR determination from Is repeatability of metabolic rate influenced by social separation? A test with a teleost fish

description: Metabolic rates are typically thought to have important influences on fitness and more broadly be relevant to the ecology and evolution of animals. Previous studies demonstrate that metabolic rates are repeatable to a certain extent under constant conditions, but how social conditions influence the repeatability of metabolic rate remains largely unknown. In this study, we investigated the repeatability of resting metabolic rate (RMR) in the highly social crucian carp (<i>Carassius auratus</i>) after being socially separated for different time periods relative to control fish that were not socially separated. We found that RMR was repeatable in fish in the control group, while the repeatability of RMR disappeared quickly (even within 7 days) when fish were exposed to social separation. This study is the first to examine the role of social separation at different time periods on the repeatability of intra-individual physiological variation in fish. We highlight that the inter-individual repeatability of metabolic rate can be substantial over time but was eliminated by social separation. The findings indicate that the repeatability of metabolic rate in fish is condition dependent, and that the change in repeatability of metabolic rate should not be overlooked when considering the ecological and evolutionary effects of environmental change.
DOI: 10.6084/m9.figshare.12128820
title: Supplementary material-Raw data for RMR determination from Is repeatability of metabolic rate influenced by social separation? A test with a teleost fish

description: Metabolic rates are typically thought to have important influences on fitness and more broadly be relevant to the ecology and evolution of animals. Previous studies demonstrate that metabolic rates are repeatable to a certain extent under constant conditions, but how social conditions influence the repeatability of metabolic rate remains largely unknown. In this study, we investigated the repeatability of resting metabolic rate (RMR) in the highly social crucian carp (<i>Carassius auratus</i>) after being socially separated for different time periods relative to control fish that were not socially separated. We found that RMR was repeatable in fish in the control group, while the repeatability of RMR disappeared quickly (even within 7 days) when fish were exposed to social separation. This study is the first to examine the role of social separation at different time periods on the repeatability of intra-individual physiological variation in fish. We highlight that the inter-individual repeatability of metabolic rate can be substantial over time but was eliminated by social separation. The findings indicate that the repeatability of metabolic rate in fish is condition dependent, and that the change in repeatability of metabolic rate should not be overlooked when considering the ecological and evolutionary effects of environmental change.
DOI: 10.6084/m9.figshare.12128886
title: Syntheses, X-ray crystal structures and catalytic epoxidation of oxidovanadium(V) and dioxidomolybdenum(VI) complexes derived from <i>N′</i>-(4-Bromo-2-hydroxybenzylidene)benzohydrazide

description: A new mononuclear oxidovanadium(V) complex [VOL(OCH<sub>3</sub>)(CH<sub>3</sub>OH)] (<b>1</b>), and a new mononuclear dioxidomolybdenum(VI) complex [MoO<sub>2</sub>L(CH<sub>3</sub>OH)] (<b>2</b>), where H<sub>2</sub>L=<i>N′</i>-(4-bromo-2-hydroxybenzylidene)benzohydrazide, have been synthesized and characterized on the basis of CHN elemental analysis, FT-IR and UV–Vis spectra. Structures of the complexes were further characterized by single crystal X-ray diffraction, which indicated that the V and Mo atoms in the complexes adopt octahedral coordination. The hydrazone behaves as a NOO tridentate ligand. The catalytic epoxidation properties on cyclooctene of the complexes were investigated.
DOI: 10.6084/m9.figshare.16847475.v1
title: Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients

description: Accumulating evidence has shown many similarities and differences of gene profiles and pathways between pediatric and adult ulcerative colitis (UC) patients. In this study, we aimed to investigate the shared genes and pathways in intestinal tissues of pediatric and adult UC. Differentially expressed genes (DEGs) between pediatric and adult UC were identified <i>via</i> bioinformatic analysis of Gene Expression Omnibus datasets GSE87473 and GSE126124. Gene Ontology and pathway enrichment were used to analyze overlapped and distinguished DEGs. Gene Set Variation Analysis (GSVA) was utilized for contrast consistency. Mice colitis models were induced by dextran sulfate sodium (DSS) and <i>Citrobacter rodentium</i>. 2616 DEGs were screened out in intestinal tissues of adult UC compared with those of adult healthy controls, and 1195 DEGs in pediatrics. Same pathways between pediatric and adult UC were enriched using overlapped DEGs, mainly related to immune responses and metabolic processes, including butyrate metabolism, which was also identified by GSVA analysis. Of note, butyrate metabolism was the exclusive down-regulated pathway enriched by these two analyses, indicating that butyrate metabolism is one of the key pathways associated with both pediatric and adult UC. In addition, butyrate suppressed DSS-induced and <i>Citrobacter rodentium</i>-induced intestinal inflammation in mice. Therefore, the study revealed that butyrate metabolism was critical in both pediatric and adult UC. And butyrate suppressed colitis in mice, which provided a theoretical basis for the potential treatment of butyrate for UC patients. <b>Abbreviations:</b> UC, Ulcerative colitis; IBD, Inflammatory bowel disease; DEGs, Differentially expressed genes; GEO, Gene Expression Omnibus; SVA, Spatial variant apodization; LIMMA, Linear models for the microarray data; FC, Fold change; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; GSVA, Gene Set Variation Analysis; MSigDB, Molecular Signatures Database; WT, Wild-type; DSS, Dextran sulfate sodium; HC, Healthy control; SD, Standard deviation; SNHG5, Small nucleolar RNA host gene 5; GLP-2, Glucagon-like peptide 2; GSE, Gene set enrichment; ECM, Extracellular matrix; TCA, Tricarboxylic acid cycle; NA, Not available.
DOI: 10.6084/m9.figshare.16847475
title: Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients

description: Accumulating evidence has shown many similarities and differences of gene profiles and pathways between pediatric and adult ulcerative colitis (UC) patients. In this study, we aimed to investigate the shared genes and pathways in intestinal tissues of pediatric and adult UC. Differentially expressed genes (DEGs) between pediatric and adult UC were identified <i>via</i> bioinformatic analysis of Gene Expression Omnibus datasets GSE87473 and GSE126124. Gene Ontology and pathway enrichment were used to analyze overlapped and distinguished DEGs. Gene Set Variation Analysis (GSVA) was utilized for contrast consistency. Mice colitis models were induced by dextran sulfate sodium (DSS) and <i>Citrobacter rodentium</i>. 2616 DEGs were screened out in intestinal tissues of adult UC compared with those of adult healthy controls, and 1195 DEGs in pediatrics. Same pathways between pediatric and adult UC were enriched using overlapped DEGs, mainly related to immune responses and metabolic processes, including butyrate metabolism, which was also identified by GSVA analysis. Of note, butyrate metabolism was the exclusive down-regulated pathway enriched by these two analyses, indicating that butyrate metabolism is one of the key pathways associated with both pediatric and adult UC. In addition, butyrate suppressed DSS-induced and <i>Citrobacter rodentium</i>-induced intestinal inflammation in mice. Therefore, the study revealed that butyrate metabolism was critical in both pediatric and adult UC. And butyrate suppressed colitis in mice, which provided a theoretical basis for the potential treatment of butyrate for UC patients. <b>Abbreviations:</b> UC, Ulcerative colitis; IBD, Inflammatory bowel disease; DEGs, Differentially expressed genes; GEO, Gene Expression Omnibus; SVA, Spatial variant apodization; LIMMA, Linear models for the microarray data; FC, Fold change; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes; GSVA, Gene Set Variation Analysis; MSigDB, Molecular Signatures Database; WT, Wild-type; DSS, Dextran sulfate sodium; HC, Healthy control; SD, Standard deviation; SNHG5, Small nucleolar RNA host gene 5; GLP-2, Glucagon-like peptide 2; GSE, Gene set enrichment; ECM, Extracellular matrix; TCA, Tricarboxylic acid cycle; NA, Not available.
DOI: 10.6084/m9.figshare.16847481
title: Silencing circular RNA circ_0054537 and upregulating microRNA-640 suppress malignant progression of renal cell carcinoma via regulating neuronal pentraxin-2 (NPTX2)

description: Hsa_circ_0054537 (circ_0054537) is a novel tumor-related circular RNA in renal cell carcinoma (RCC), and we intended to ascertain its dysregulation and functions in RCC malignant progression, as well as the underlying mechanism via serving as competing endogenous RNA (ceRNA). In this research, using real-time quantitative PCR, we found circ_0054537 was upregulated in RCC tissues and cells, and distributed throughout the cytoplasm. Then, functional effects of circ_0054537 in RCC were detected using cell counting kit-8, transwell, flow cytometry and glycolysis stress test and adenosine Triphosphate (ATP) assays. The results uncovered that circ_0054537 knockdown inhibited cell proliferation, migration, invasion, autophagy and glycolysis, but promoted apoptosis in RCC cells. Notably, circ_0054537 was identified as a ceRNA for microRNA (miR)-640, and miR-640 could target neuronal pentraxin-2 (NPTX2), as evidenced by dual-luciferase reporter assay and RNA immunoprecipitation assay. Besides, miR-640 downregulation or NPTX2 overexpression partly overturned the tumor suppressor function of circ_0054537 silence and miR-640 overexpression in RCC cells. Additionally, RCC cell growth <i>in vivo</i> was retarded by circ_0054537 silence. In conclusion, circ_0054537/miR-640/NPTX2 ceRNA pathway regulated RCC malignant progression <i>in vitro</i> and curbed RCC tumor growth <i>in vivo</i>, which could be a potential diagnosis and therapeutic target of RCC.
DOI: 10.60859/zqmm-a533
title: NG00068
DOI: 10.60859/3p10-fy87
title: NG00069
DOI: 10.34740/kaggle/dsv/7584414
title: Public Opinion Russia Ukraine War (Updated Daily)
DOI: 10.6084/m9.figshare.22614451.v1
title: Additional file 1 of Corneal thickness measurements with the RTVue, Casia-2, and Pentacam devices in patients with mild-to-moderate keratoconus: a comparative study

description: Additional file 1.
DOI: 10.60859/5xhx-4777
title: NG00070
DOI: 10.6084/m9.figshare.22614451
title: Additional file 1 of Corneal thickness measurements with the RTVue, Casia-2, and Pentacam devices in patients with mild-to-moderate keratoconus: a comparative study

description: Additional file 1.
DOI: 10.6084/m9.figshare.6885956
title: Additional file 1: of Maternal central obesity and birth size: a Mendelian randomization analysis

description: Table S1a. WHRadjBMI loci achieving genome-wide significance (P &lt; 5 × 10–8) in European women-specific meta-analyses. Table S1b. WCadjBMI loci achieving genome-wide significance (P &lt; 5 × 10–8) in European women-specific meta-analyses. Table S1c. HIPadjBMI loci achieving genome-wide significance (P &lt; 5 × 10–8) in European women-specific meta-analyses. (XLSX 22 kb)
DOI: 10.6084/m9.figshare.12128886.v1
title: Syntheses, X-ray crystal structures and catalytic epoxidation of oxidovanadium(V) and dioxidomolybdenum(VI) complexes derived from <i>N′</i>-(4-Bromo-2-hydroxybenzylidene)benzohydrazide

description: A new mononuclear oxidovanadium(V) complex [VOL(OCH<sub>3</sub>)(CH<sub>3</sub>OH)] (<b>1</b>), and a new mononuclear dioxidomolybdenum(VI) complex [MoO<sub>2</sub>L(CH<sub>3</sub>OH)] (<b>2</b>), where H<sub>2</sub>L=<i>N′</i>-(4-bromo-2-hydroxybenzylidene)benzohydrazide, have been synthesized and characterized on the basis of CHN elemental analysis, FT-IR and UV–Vis spectra. Structures of the complexes were further characterized by single crystal X-ray diffraction, which indicated that the V and Mo atoms in the complexes adopt octahedral coordination. The hydrazone behaves as a NOO tridentate ligand. The catalytic epoxidation properties on cyclooctene of the complexes were investigated.
DOI: 10.6084/m9.figshare.16847481.v1
title: Silencing circular RNA circ_0054537 and upregulating microRNA-640 suppress malignant progression of renal cell carcinoma via regulating neuronal pentraxin-2 (NPTX2)

description: Hsa_circ_0054537 (circ_0054537) is a novel tumor-related circular RNA in renal cell carcinoma (RCC), and we intended to ascertain its dysregulation and functions in RCC malignant progression, as well as the underlying mechanism via serving as competing endogenous RNA (ceRNA). In this research, using real-time quantitative PCR, we found circ_0054537 was upregulated in RCC tissues and cells, and distributed throughout the cytoplasm. Then, functional effects of circ_0054537 in RCC were detected using cell counting kit-8, transwell, flow cytometry and glycolysis stress test and adenosine Triphosphate (ATP) assays. The results uncovered that circ_0054537 knockdown inhibited cell proliferation, migration, invasion, autophagy and glycolysis, but promoted apoptosis in RCC cells. Notably, circ_0054537 was identified as a ceRNA for microRNA (miR)-640, and miR-640 could target neuronal pentraxin-2 (NPTX2), as evidenced by dual-luciferase reporter assay and RNA immunoprecipitation assay. Besides, miR-640 downregulation or NPTX2 overexpression partly overturned the tumor suppressor function of circ_0054537 silence and miR-640 overexpression in RCC cells. Additionally, RCC cell growth <i>in vivo</i> was retarded by circ_0054537 silence. In conclusion, circ_0054537/miR-640/NPTX2 ceRNA pathway regulated RCC malignant progression <i>in vitro</i> and curbed RCC tumor growth <i>in vivo</i>, which could be a potential diagnosis and therapeutic target of RCC.
DOI: 10.6084/m9.figshare.22614518
title: Additional file 1 of Genetic screening of a Chinese cohort of children with hearing loss using a next-generation sequencing panel

description: Additional file 1: Table S1. The panel containing 518 genes associated with deafness.
DOI: 10.6084/m9.figshare.22614518.v1
title: Additional file 1 of Genetic screening of a Chinese cohort of children with hearing loss using a next-generation sequencing panel

description: Additional file 1: Table S1. The panel containing 518 genes associated with deafness.
DOI: 10.6084/m9.figshare.22614524
title: Additional file 3 of Genetic screening of a Chinese cohort of children with hearing loss using a next-generation sequencing panel

description: Additional file 3: Table S3. The frequency of mutation site in 5000 normal population.