cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21839747.v1
title: CircHGS enhances the progression of bladder cancer by regulating the miR-513a-5p/VEGFC axis and activating the AKT/mTOR signaling pathway

description: Bladder cancer (BCa) is a malignant tumor that occurs in the bladder mucosa with high mortality. Circular RNAs (circRNAs), as newly discovered noncoding RNAs, are associated with the occurrence and development of BCa. However, the effects of circRNAs in BCa have not been fully elucidated. Through the GEO (Gene Expression Omnibus) database, an abnormally expressed circular RNA, circHGS (hsa_circ_0004721), was first identified in BCa. qRT – PCR was performed to measure the expression of circHGS in BCa tissues and cells. The intracellular localization of circHGS was detected by nucleocytoplasmic separation experiment and fluorescence in situ hybridization assay. <i>In vitro</i> experiments were conducted to detect the effects of circHGS on cell cycle, proliferation, migration and invasion. The correlations between miR-513a-5p and circHGS or VEGFC were confirmed by dual-luciferase reporter assay, qRT – PCR and western blot. The role of circHGS <i>in vivo</i> was verified by xenograft tumor mice model. In this study, we clarified the roles and potential mechanism of circHGS in BCa. CircHGS, originating from the HGS gene, is upregulated in BCa tissues compared to normal tissues. Moreover, the expression of circHGS in BCa was positively associated with tumor grade and pathological T stage. Functionally, silencing of circHGS apparently suppressed cell cycle, proliferation, migration and invasion, but circHGS overexpression showed the opposite result. <i>In vivo</i> experiments also suggested that knockdown of circHGS suppressed tumor growth. Mechanistically, circHGS functions as a sponge of miR-513a-5p to elevate VEGFC expression and activate the AKT/mTOR signaling pathway, ultimately promoting BCa progression. Our findings indicated that circHGS promotes BCa progression via the miR-513a-5p/VEGFC/AKT/mTOR pathway and can be a promising therapeutic target of BCa.
DOI: 10.6084/m9.figshare.21314165.v1
title: Additional file 2 of Cross-watershed distribution pattern challenging the elimination of Oncomelania hupensis, the intermediate host of Schistosoma japonica, in Sichuan province, China

description: Additional file 2: Dataset S1. The 130 unique cox1 haplotypes of Oncomelania hupensis from this study including two outgroups
DOI: 10.6084/m9.figshare.11352575.v1
title: MOESM1 of Comparative transcriptome and histological analyses of wheat in response to phytotoxic aphid Schizaphis graminum and non-phytotoxic aphid Sitobion avenae feeding

description: Additional file 1: Table S1. Summary of transcriptome data.
DOI: 10.6084/m9.figshare.11352584.v1
title: MOESM2 of Comparative transcriptome and histological analyses of wheat in response to phytotoxic aphid Schizaphis graminum and non-phytotoxic aphid Sitobion avenae feeding

description: Additional file 2: Data S1. List of all DEGs after infestation by aphids in comparison with controls.
DOI: 10.6084/m9.figshare.11352608.v1
title: MOESM5 of Comparative transcriptome and histological analyses of wheat in response to phytotoxic aphid Schizaphis graminum and non-phytotoxic aphid Sitobion avenae feeding

description: Additional file 5: Data S3. Transcript levels of genes involved in ROS scavenge after aphid feeding.
DOI: 10.6084/m9.figshare.11352623.v1
title: MOESM6 of Cytological and transcriptome analyses reveal OsPUB73 defect affects the gene expression associated with tapetum or pollen exine abnormality in rice

description: Additional file 6: Table S2. The correlation analysis between all samples.
DOI: 10.6084/m9.figshare.19738597
title: Additional file 1 of Combined morpho-physiological, ionomic and transcriptomic analyses reveal adaptive responses of allohexaploid wheat (Triticum aestivum L.) to iron deficiency

description: Additional file: Table S1. Names of wheat accessions used in this study.
DOI: 10.6084/m9.figshare.19738597.v1
title: Additional file 1 of Combined morpho-physiological, ionomic and transcriptomic analyses reveal adaptive responses of allohexaploid wheat (Triticum aestivum L.) to iron deficiency

description: Additional file: Table S1. Names of wheat accessions used in this study.
DOI: 10.6084/m9.figshare.6635471
title: Pollen-food allergy syndrome in China

description: Little is known about pollen-food allergy syndrome (PFS) in China. To investigate the clinical characteristics, as well as sensitization patterns, of PFS in China. Clinical parameters and serum Immunoglobulin E (IgE) responses to prevalent pollens, plant foods and corresponding allergen components were evaluated. The top three most common pollen-associated allergenic foods were peach, apple and pear. Fifty-nine percent of the patients with PFS were allergic to peach. Sixty-one percent of PFS patients developed systemic reactions with or without oral cavity discomfort upon ingestion of the culprit food. Positive IgE responses to nonspecific lipid transfer proteins occurred in 69.9% of PFS patients, which was in accordance with the high prevalence of systemic reactions. Peach was the most common allergenic food in PFS patients. Patients with PFS in China showed an LTP-dominant sensitization profile and usually presented systemic reactions upon consumption of the allergenic foods.
DOI: 10.6084/m9.figshare.6635471.v1
title: Pollen-food allergy syndrome in China

description: Little is known about pollen-food allergy syndrome (PFS) in China. To investigate the clinical characteristics, as well as sensitization patterns, of PFS in China. Clinical parameters and serum Immunoglobulin E (IgE) responses to prevalent pollens, plant foods and corresponding allergen components were evaluated. The top three most common pollen-associated allergenic foods were peach, apple and pear. Fifty-nine percent of the patients with PFS were allergic to peach. Sixty-one percent of PFS patients developed systemic reactions with or without oral cavity discomfort upon ingestion of the culprit food. Positive IgE responses to nonspecific lipid transfer proteins occurred in 69.9% of PFS patients, which was in accordance with the high prevalence of systemic reactions. Peach was the most common allergenic food in PFS patients. Patients with PFS in China showed an LTP-dominant sensitization profile and usually presented systemic reactions upon consumption of the allergenic foods.
DOI: 10.6084/m9.figshare.8207087.v1
title: Additional file 10: of Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

description: Table S6. Summary of the EST-SSRs identified from the orthogroups in the nine Diospyros samples. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8207096
title: Additional file 11: of Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

description: Table S7. Characteristics of the 120 conserved microsatellites primers based on orthologs in the DK species. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.11352647.v1
title: MOESM3 of Investigating RNA expression profiles altered by nicotinamide mononucleotide therapy in a chronic model of alcoholic liver disease

description: Additional file 3: Table S2: RNA-seq.
DOI: 10.6084/m9.figshare.8207099.v1
title: Additional file 1: of Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

description: Alignments of 861,013 amino acid sequences from the tandem 2603 one-to-one single copy gene. (FASTA 2522 kb)
DOI: 10.6084/m9.figshare.21314231.v1
title: Additional file 3 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

description: Additional file 3.
DOI: 10.6084/m9.figshare.15022766.v1
title: CAMK2/CaMKII activates MLKL in short-term starvation to facilitate autophagic flux

description: MLKL (mixed lineage kinase domain like pseudokinase) is a well-known core component of necrosome that executes necroptotic cell death upon phosphorylation by RIPK3 (receptor interacting serine/threonine kinase 3). Recent studies also implicate a role of MLKL in endosomal trafficking, which is not always dependent on RIPK3. Using mouse Neuro-2a and L929 as well as human HEK293 and HT29 cells, we show here that MLKL is phosphorylated in response to serum and amino acid deprivation from the culture medium, in a manner that depends on CAMK2/CaMKII (calcium/calmodulin dependent protein kinase II) but not RIPK3. The starvation-induced increase in MLKL phosphorylation was accompanied by decreases in levels of lipidated MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta; LC3-II) and SQSTM1/p62 (sequestosome 1), markers of autophagosomes. These changes were prevented by disrupting either MLKL or CAMK2 by pharmacology and genetic manipulations. Moreover, disrupting MLKL or CAMK2 also inhibited the incorporation of LC3-II into autolysosomes, demonstrating a role of the CAMK2-MLKL pathway in facilitating autophagic flux during short-term starvation, in contrast to necroptosis which suppressed autophagic flux. Furthermore, unlike the necroptotic pathway, the starvation-evoked CAMK2-mediated MLKL phosphorylation protected cells from starvation-induced death. We propose that upon nutrient deprivation, MLKL is activated by CAMK2, which in turn facilitates membrane scission needed for autophagosome maturation, allowing the proper fusion of the autophagosome with lysosome and the subsequent substance degradation. This novel function is independent of RIPK3 and is not involved in necroptosis, implicating new roles for this pseudokinase in cell survival, signaling and metabolism. <b>Abbreviations:</b> CAMK2/CaMKII: calcium/calmodulin dependent protein kinase II; DIABLO/SMAC: direct inhibitor of apoptosis-binding protein with low pI/second mitochondria-derived activator of caspase; ECS: extracellular solution; ESCRT: endosomal sorting complexes required for transport; FBS: fetal bovine serum; GSK3B: glycogen synthase kinase 3 beta; HBSS: Hanks’ balanced salt solution; KO: knockout; LC3-II: lipidated microtubule associated protein 1 light chain 3 beta; LDH: lactate dehydrogenase; MLKL: mixed lineage kinase domain like pseudokinase; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; N2a: Neuro-2a neuroblastoma; Nec-1: necrostatin-1; NSA: necrosulfonamide; PBS: phosphate-buffered saline; PI: propidium iodide; PK-hLC3: pHluorin-mKate2-human LC3; RIPK1: receptor interacting serine/threonine kinase 1; RIPK3: receptor interacting serine/threonine kinase 3; ROS: reactive oxygen species; RPS6KB1/S6K: ribosomal protein S6 kinase B1; shRNA: short hairpin RNA; siRNA: small interference RNA; SQSTM1/p62: sequestosome 1; TBS: Tris-buffered saline; TNF/TNF-α: tumor necrosis factor; TSZ, treatment with TNF + DIABLO mimetics + z-VAD-FMK.
DOI: 10.6084/m9.figshare.21314165
title: Additional file 2 of Cross-watershed distribution pattern challenging the elimination of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in Sichuan province, China

description: Additional file 2: Dataset S1. The 130 unique cox1 haplotypes of Oncomelania hupensis from this study including two outgroups
DOI: 10.6084/m9.figshare.21314165.v2
title: Additional file 2 of Cross-watershed distribution pattern challenging the elimination of Oncomelania hupensis, the intermediate host of Schistosoma japonicum, in Sichuan province, China

description: Additional file 2: Dataset S1. The 130 unique cox1 haplotypes of Oncomelania hupensis from this study including two outgroups
DOI: 10.6084/m9.figshare.21314228.v1
title: Additional file 2 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

description: Additional file 2.
DOI: 10.6084/m9.figshare.4012740
title: Expression of CD56 is a risk factor for acute lymphocytic leukemia with central nervous system involvement in adults

description: <b>Objective:</b> To gain further insights into the predisposing risk factors for central nervous system (CNS) involvement in patients with acute lymphocytic leukemia (ALL), the impact of CD56 expression in these patients was investigated. <b>Methods:</b> We reviewed the clinical features of CD56 expression in 588 consecutive ALL patients treated with systemic chemotherapy regimens between 2000 and 2014. The categorical data from CD56<sup>+</sup> ALL patients were compared with those from CD56<sup>−</sup> ALL patients. <b>Results:</b> Among the 588 patients studied, 18.9% showed CD56 expression. The expression was significantly associated with CD33<sup>+</sup>, CD10<sup>−</sup>, CD15<sup>+</sup>, TdT<sup>−</sup>, and CD5<sup>+</sup> immunophenotypes. After systemic chemotherapy, 8.8% patients showed CNS involvement, of which 3.2% exhibited combined recurrences and 5.6% exhibited isolated CNS involvement. The 5-year event-free survival was significantly lower for patients with CD56<sup>+</sup> immunophenotype compared with patients with CD56<sup>−</sup> immunophenotype (22.5% vs. 32.7%, <i>P</i> = 0.04). Cumulative incidences of CNS involvement were significantly greater in the CD56<sup>+</sup> cohort compared with the CD56<sup>−</sup> cohort (14.4% vs. 7.5%, <i>P</i> = 0.02). Multivariate analysis revealed CD56 expression to be statistically significant risk factors for CNS involvement. <b>Conclusion:</b> CD56 expression should be regarded as an independent risk factor for ALL with CNS involvement in adults.
DOI: 10.6084/m9.figshare.21314234.v1
title: Additional file 4 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

description: Additional file 4.
DOI: 10.6084/m9.figshare.11352731.v1
title: MOESM1 of Schistosoma haematobium infection morbidity, praziquantel effectiveness and reinfection rate among children and young adults in Gabon

description: Additional file 1: Table S1. Name and modalities of each variable included in the analysis. Table S2. Database used for the longitudinal analysis. Table S3. Database used for drug efficacy assessment. Table S4. Database used for the survival analysis.
DOI: 10.6084/m9.figshare.4012740.v1
title: Expression of CD56 is a risk factor for acute lymphocytic leukemia with central nervous system involvement in adults

description: <b>Objective:</b> To gain further insights into the predisposing risk factors for central nervous system (CNS) involvement in patients with acute lymphocytic leukemia (ALL), the impact of CD56 expression in these patients was investigated. <b>Methods:</b> We reviewed the clinical features of CD56 expression in 588 consecutive ALL patients treated with systemic chemotherapy regimens between 2000 and 2014. The categorical data from CD56<sup>+</sup> ALL patients were compared with those from CD56<sup>−</sup> ALL patients. <b>Results:</b> Among the 588 patients studied, 18.9% showed CD56 expression. The expression was significantly associated with CD33<sup>+</sup>, CD10<sup>−</sup>, CD15<sup>+</sup>, TdT<sup>−</sup>, and CD5<sup>+</sup> immunophenotypes. After systemic chemotherapy, 8.8% patients showed CNS involvement, of which 3.2% exhibited combined recurrences and 5.6% exhibited isolated CNS involvement. The 5-year event-free survival was significantly lower for patients with CD56<sup>+</sup> immunophenotype compared with patients with CD56<sup>−</sup> immunophenotype (22.5% vs. 32.7%, <i>P</i> = 0.04). Cumulative incidences of CNS involvement were significantly greater in the CD56<sup>+</sup> cohort compared with the CD56<sup>−</sup> cohort (14.4% vs. 7.5%, <i>P</i> = 0.02). Multivariate analysis revealed CD56 expression to be statistically significant risk factors for CNS involvement. <b>Conclusion:</b> CD56 expression should be regarded as an independent risk factor for ALL with CNS involvement in adults.
DOI: 10.6084/m9.figshare.23937271
title: Additional file 1 of Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus

description: Additional file 1: Tab. S1. Primer sequence used in the real-time PCR.
DOI: 10.6084/m9.figshare.23937271.v1
title: Additional file 1 of Comparative transcriptomic analysis of reproductive characteristics of reciprocal hybrid lineages derived from hybridization between Megalobrama amblycephala and Culter alburnus

description: Additional file 1: Tab. S1. Primer sequence used in the real-time PCR.
DOI: 10.6084/m9.figshare.15022766
title: CAMK2/CaMKII activates MLKL in short-term starvation to facilitate autophagic flux

description: MLKL (mixed lineage kinase domain like pseudokinase) is a well-known core component of necrosome that executes necroptotic cell death upon phosphorylation by RIPK3 (receptor interacting serine/threonine kinase 3). Recent studies also implicate a role of MLKL in endosomal trafficking, which is not always dependent on RIPK3. Using mouse Neuro-2a and L929 as well as human HEK293 and HT29 cells, we show here that MLKL is phosphorylated in response to serum and amino acid deprivation from the culture medium, in a manner that depends on CAMK2/CaMKII (calcium/calmodulin dependent protein kinase II) but not RIPK3. The starvation-induced increase in MLKL phosphorylation was accompanied by decreases in levels of lipidated MAP1LC3B/LC3B (microtubule associated protein 1 light chain 3 beta; LC3-II) and SQSTM1/p62 (sequestosome 1), markers of autophagosomes. These changes were prevented by disrupting either MLKL or CAMK2 by pharmacology and genetic manipulations. Moreover, disrupting MLKL or CAMK2 also inhibited the incorporation of LC3-II into autolysosomes, demonstrating a role of the CAMK2-MLKL pathway in facilitating autophagic flux during short-term starvation, in contrast to necroptosis which suppressed autophagic flux. Furthermore, unlike the necroptotic pathway, the starvation-evoked CAMK2-mediated MLKL phosphorylation protected cells from starvation-induced death. We propose that upon nutrient deprivation, MLKL is activated by CAMK2, which in turn facilitates membrane scission needed for autophagosome maturation, allowing the proper fusion of the autophagosome with lysosome and the subsequent substance degradation. This novel function is independent of RIPK3 and is not involved in necroptosis, implicating new roles for this pseudokinase in cell survival, signaling and metabolism. <b>Abbreviations:</b> CAMK2/CaMKII: calcium/calmodulin dependent protein kinase II; DIABLO/SMAC: direct inhibitor of apoptosis-binding protein with low pI/second mitochondria-derived activator of caspase; ECS: extracellular solution; ESCRT: endosomal sorting complexes required for transport; FBS: fetal bovine serum; GSK3B: glycogen synthase kinase 3 beta; HBSS: Hanks’ balanced salt solution; KO: knockout; LC3-II: lipidated microtubule associated protein 1 light chain 3 beta; LDH: lactate dehydrogenase; MLKL: mixed lineage kinase domain like pseudokinase; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; N2a: Neuro-2a neuroblastoma; Nec-1: necrostatin-1; NSA: necrosulfonamide; PBS: phosphate-buffered saline; PI: propidium iodide; PK-hLC3: pHluorin-mKate2-human LC3; RIPK1: receptor interacting serine/threonine kinase 1; RIPK3: receptor interacting serine/threonine kinase 3; ROS: reactive oxygen species; RPS6KB1/S6K: ribosomal protein S6 kinase B1; shRNA: short hairpin RNA; siRNA: small interference RNA; SQSTM1/p62: sequestosome 1; TBS: Tris-buffered saline; TNF/TNF-α: tumor necrosis factor; TSZ, treatment with TNF + DIABLO mimetics + z-VAD-FMK.
DOI: 10.6084/m9.figshare.21314228
title: Additional file 2 of The long non-coding RNA lncMYOZ2 mediates an AHCY/MYOZ2 axis to promote adipogenic differentiation in porcine preadipocytes

description: Additional file 2.
DOI: 10.6084/m9.figshare.15020474.v1
title: Additional file 1 of RNA-seq co-expression network analysis reveals anxiolytic behavior of mice with Efnb2 knockout in parvalbumin+ neurons

description: Additional file 1. Summary of assembly statistics after Illumina sequencing.
DOI: 10.6084/m9.figshare.8207066
title: Additional file 1: of Feeding difficulty is the dominant feature in 12 Chinese newborns with CHD7 pathogenic variants

description: Table S1. Filtered variations of 12 patients. (XLS 552 kb)
DOI: 10.6084/m9.figshare.19217190
title: Comparison of transcriptome profiles of nucleated red blood cells in cord blood between preterm and full-term neonates

description: The reactivation of fetal γ-globin expression is an effective strategy for ameliorating the clinical symptoms of β-hemoglobinopathies. However, the mechanism of globin switching, especially the roles of long non-coding RNAs (lncRNAs) in this process, remains elusive. We compared the <i>in vivo</i> transcriptome profiles of nucleated red blood cells (NRBCs) isolated from the umbilical cord blood of preterm and full-term newborns. We collected 75 umbilical cord blood samples and performed qPCR of the candidate genes. In this study, we identified 7,166 differentially expressed protein-coding genes, 3,243 differentially expressed lncRNAs, and 79 differentially expressed microRNAs. Our data show that the Fanconi anemia pathway and the H19/let-7/LIN28B axis may be involved in γ- to β-globin gene switching. Moreover, we constructed the hub gene network of the differentially expressed transcription factors. Based on qPCR, we found that <i>BCL11A</i> was differentially expressed based on biological sex. We also confirmed that <i>H19</i> is differentially expressed and established the H19-related network to reveal the potential regulatory mechanisms. We present the profiles of the <i>in vivo</i> transcriptome differences of NRBCs between preterm and full-term neonates for the first time, and provide novel research targets for β-hemoglobinopathies.
DOI: 10.6084/m9.figshare.19217190.v1
title: Comparison of transcriptome profiles of nucleated red blood cells in cord blood between preterm and full-term neonates

description: The reactivation of fetal γ-globin expression is an effective strategy for ameliorating the clinical symptoms of β-hemoglobinopathies. However, the mechanism of globin switching, especially the roles of long non-coding RNAs (lncRNAs) in this process, remains elusive. We compared the <i>in vivo</i> transcriptome profiles of nucleated red blood cells (NRBCs) isolated from the umbilical cord blood of preterm and full-term newborns. We collected 75 umbilical cord blood samples and performed qPCR of the candidate genes. In this study, we identified 7,166 differentially expressed protein-coding genes, 3,243 differentially expressed lncRNAs, and 79 differentially expressed microRNAs. Our data show that the Fanconi anemia pathway and the H19/let-7/LIN28B axis may be involved in γ- to β-globin gene switching. Moreover, we constructed the hub gene network of the differentially expressed transcription factors. Based on qPCR, we found that <i>BCL11A</i> was differentially expressed based on biological sex. We also confirmed that <i>H19</i> is differentially expressed and established the H19-related network to reveal the potential regulatory mechanisms. We present the profiles of the <i>in vivo</i> transcriptome differences of NRBCs between preterm and full-term neonates for the first time, and provide novel research targets for β-hemoglobinopathies.
DOI: 10.6084/m9.figshare.8207099
title: Additional file 1: of Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

description: Alignments of 861,013 amino acid sequences from the tandem 2603 one-to-one single copy gene. (FASTA 2522 kb)
DOI: 10.6084/m9.figshare.17119991
title: Additional file 1 of An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing

description: Additional file 1. Supplementary tables. Table S1: The list of somatic mutations previously identified from dual-platform single-cell whole-exome sequencing used for the current evaluation. Table S2: The summary of the comparison between the Agilent- and Nextera-runs using different negative-defining methods.