cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11956005.v5
title: Protective effect of brain-derived neurotrophic factor and neurotrophin-3 overexpression by adipose-derived stem cells combined with silk fibroin/chitosan scaffold in spinal cord injury

description: <b>Objectives</b>: Spinal cord injury (SCI) is a most debilitating traumatic injury, and cytotherapy is a promising alternative treatment strategy. Here we investigated the effect and mechanism of adipose-derived stem/stromal cells (ASCs) with overexpressing brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT3) (BDNF-NT3) in combination with silk fibroin/chitosan scaffold (SFCS) in SCI. <b>Methods</b>: Female Sprague-Dawley rats were used as an SCI model. SFCS,SFCS and ASCs, or ASCs overexpressing NT3, BDNF, and BDNF-NT3 were implanted into SCI rats. Basso, Beattie, and Bresnahan score, pathological changes, and spinal cord tissue and nerve fiber morphology were observed and assayed. GAP-43, GFAP, and caspase-3 expression was determined using immunohistochemistry and western blotting. <b>Results</b>: Smoother spinal cords, less scar tissue, and lower inflammatory activity were found in the SFCS, SFCS and ASCs, ASCs with NT3, BDNF, and BDNF-NT3 overexpression treatment than in the untreated SCI rat groups. Increasing formation of nerve fibers was observed in the above groups in order. GAP-43 expression significantly increased, while GFAP and caspase-3 expression significantly decreased. These results indicated obvious alleviation in pathological changes and BDNF-NT3 overexpression in ASCs combined with SFCS treatment in SCI rats. <b>Conclusion</b>: Thus, BDNF-NT3 overexpression from ASCs with SFCS had synergistic neuroprotective effects on SCI and may be a treatment option for SCI.
DOI: 10.6084/m9.figshare.6188843
title: Research Front Detection and Topic Evolution Based on Topological Structure and PageRank Algorithm

description: this is the data used in my article "research front detection and topic evolution based on topological structure and PageRank algorithm". The data include the scientific documents in Dataset I (D1.txt), the scientific documents
in Dataset II (D2.txt), the scientific documents in Dataset I without isolated
document (D3.txt), and the scientific documents in Dataset II without isolated
document (D4.txt), the unique number of scientific documents (D5.txt), the similarity
between scientific documents for document clustering (D6.txt), and the
similarity between clusters for topic evolution (D7.txt).
DOI: 10.6084/m9.figshare.14053161
title: Additional file 1 of A Semi-Dominant Mutation in OsCESA9 Improves Salt Tolerance and Favors Field Straw Decay Traits by Altering Cell Wall Properties in Rice

description: Additional file 1.
DOI: 10.6084/m9.figshare.14053161.v1
title: Additional file 1 of A Semi-Dominant Mutation in OsCESA9 Improves Salt Tolerance and Favors Field Straw Decay Traits by Altering Cell Wall Properties in Rice

description: Additional file 1.
DOI: 10.6084/m9.figshare.11956029
title: A novel Co(II)-based coordination polymer: crystal structure and biological activity

description: Based on a mixed-ligand strategy, a new coordination polymer with the chemical formula of {[Co<sub>2</sub>(IMMB)<sub>2</sub>(bim)]·2DMA}<sub>n</sub> (<b>1</b>, DMA = N,N-dimethylacetamide) has been successfully synthesized by the reaction of 4,4’-((1H-imidazol-1-yl)methylene)dibenzoic acid (H<sub>2</sub>IMMB) and Co(NO<sub>3</sub>)<sub>2</sub>·6H<sub>2</sub>O with the presence of benzimidazole as the co-ligand under the solvothermal methods. Furthermore, a green hand grinding technique has been implemented to reduce the particle size of the complex <b>1</b> to generate nanoscale <b>1</b> (denoted as nano <b>1</b> hereafter) with rod-like morphology. Furthermore, the protective of nano <b>1</b> on the acute peritonitis complicated peritonitis was evaluated. Firstly, the inhibitory effect of nano <b>1</b> on the <i>yigP</i> gene expression was measured by reverse transcription-polymerase chain reaction (RT-PCR), which is vital important for the <i>E. coli</i> viability. Next, the protective ability of nano <b>1</b> in the children acute peritonitis complicated peritonitis animal model was evaluated by detecting the content of the inflammatory cytokines through enzyme linked immunosorbent assay (ELISA).
DOI: 10.6084/m9.figshare.11956029.v1
title: A novel Co(II)-based coordination polymer: crystal structure and biological activity

description: Based on a mixed-ligand strategy, a new coordination polymer with the chemical formula of {[Co<sub>2</sub>(IMMB)<sub>2</sub>(bim)]·2DMA}<sub>n</sub> (<b>1</b>, DMA = N,N-dimethylacetamide) has been successfully synthesized by the reaction of 4,4’-((1H-imidazol-1-yl)methylene)dibenzoic acid (H<sub>2</sub>IMMB) and Co(NO<sub>3</sub>)<sub>2</sub>·6H<sub>2</sub>O with the presence of benzimidazole as the co-ligand under the solvothermal methods. Furthermore, a green hand grinding technique has been implemented to reduce the particle size of the complex <b>1</b> to generate nanoscale <b>1</b> (denoted as nano <b>1</b> hereafter) with rod-like morphology. Furthermore, the protective of nano <b>1</b> on the acute peritonitis complicated peritonitis was evaluated. Firstly, the inhibitory effect of nano <b>1</b> on the <i>yigP</i> gene expression was measured by reverse transcription-polymerase chain reaction (RT-PCR), which is vital important for the <i>E. coli</i> viability. Next, the protective ability of nano <b>1</b> in the children acute peritonitis complicated peritonitis animal model was evaluated by detecting the content of the inflammatory cytokines through enzyme linked immunosorbent assay (ELISA).
DOI: 10.6084/m9.figshare.16674620.v1
title: Additional file 1 of Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize

description: Additional file 1: Table S1. Total proteins identified in waxy maize kernels.
DOI: 10.6084/m9.figshare.16674623
title: Additional file 2 of Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize

description: Additional file 2: Table S2. Total differentially accumulated proteins identified at 10 dap and 25 dap.
DOI: 10.6084/m9.figshare.16674620
title: Additional file 1 of Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize

description: Additional file 1: Table S1. Total proteins identified in waxy maize kernels.
DOI: 10.6084/m9.figshare.16674623.v1
title: Additional file 2 of Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize

description: Additional file 2: Table S2. Total differentially accumulated proteins identified at 10 dap and 25 dap.
DOI: 10.6084/m9.figshare.14577487
title: Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p

description: Although long non-coding RNA (LncRNA) LINC00649 is reported to be closely associated with acute myeloid leukemia (AML), prostate cancer and colorectal cancer, its role in regulating other types of cancer, such as gastric cancer (GC), has not been studied. This study analyzed the expression status of LINC00649 in GC tissues and cells by performing Real-Time qPCR analysis, and we found that LINC00649 tended to be enriched in cancerous tissues and cells but not in their normal counterparts, which were supported by the data from TCGA dataset. Next, by performing the gain- and loss-of-function experiments, we expectedly found that LINC00649 acted as an oncogene to accelerate GC cell proliferation, migration and epithelial-mesenchymal transition (EMT) <i>in vitro</i> and promote its tumorigenesis <i>in vivo</i>. Moreover, the online miRDB software predicted that miR-16-5p bound to both LINC00649 and 3ʹ untranslated region (3ʹUTR) of YAP1 mRNA, which were validated by the following dual-luciferase reporter gene system assay and RNA pull-down assay. Finally, we proved that LINC00649 exerted its tumor-promoting effects in GC by regulating the miR-16-5p/YES-associated protein 1 (YAP1)/Hippo pathway. Mechanistically, knock-down of LINC00649 suppressed YAP1 expressions by releasing miR-16-5p, resulting in the recovery of the Hippo pathway, which suppressed the expression levels of the downstream oncogenes, including EGFR, SOX2 and OCT4, leading to the inhibition of the malignant phenotypes in GC cells. In conclusion, this study, for the first time, evidenced that LINC00649 promoted GC progression by targeting the miR-16-5p/YAP1/Hippo signaling pathway, which provided potential diagnostic and therapeutic indicators for GC treatment for clinical utilization.
DOI: 10.6084/m9.figshare.14577487.v1
title: Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p

description: Although long non-coding RNA (LncRNA) LINC00649 is reported to be closely associated with acute myeloid leukemia (AML), prostate cancer and colorectal cancer, its role in regulating other types of cancer, such as gastric cancer (GC), has not been studied. This study analyzed the expression status of LINC00649 in GC tissues and cells by performing Real-Time qPCR analysis, and we found that LINC00649 tended to be enriched in cancerous tissues and cells but not in their normal counterparts, which were supported by the data from TCGA dataset. Next, by performing the gain- and loss-of-function experiments, we expectedly found that LINC00649 acted as an oncogene to accelerate GC cell proliferation, migration and epithelial-mesenchymal transition (EMT) <i>in vitro</i> and promote its tumorigenesis <i>in vivo</i>. Moreover, the online miRDB software predicted that miR-16-5p bound to both LINC00649 and 3ʹ untranslated region (3ʹUTR) of YAP1 mRNA, which were validated by the following dual-luciferase reporter gene system assay and RNA pull-down assay. Finally, we proved that LINC00649 exerted its tumor-promoting effects in GC by regulating the miR-16-5p/YES-associated protein 1 (YAP1)/Hippo pathway. Mechanistically, knock-down of LINC00649 suppressed YAP1 expressions by releasing miR-16-5p, resulting in the recovery of the Hippo pathway, which suppressed the expression levels of the downstream oncogenes, including EGFR, SOX2 and OCT4, leading to the inhibition of the malignant phenotypes in GC cells. In conclusion, this study, for the first time, evidenced that LINC00649 promoted GC progression by targeting the miR-16-5p/YAP1/Hippo signaling pathway, which provided potential diagnostic and therapeutic indicators for GC treatment for clinical utilization.
DOI: 10.6084/m9.figshare.14577495
title: Circulating microRNA profile unveils mechanisms of action of acitretin for psoriasis vulgaris

description: Psoriasis vulgaris is a common chronic and recurrent inflammatory skin disease. In clinical practice, acitretin is the first-line treatment drug for psoriasis vulgaris. MicroRNAs (miRNAs) play a vital role in the initiation and development of psoriasis vulgaris. However few studies focused on the mechanisms of acitretin in the treatment of psoriasis vulgaris from the perspective of miRNAs. Here, the expression profiles of circulating miRNAs in the plasma of 12 patients with psoriasis vulgaris before and after acitretin treatment were sequenced. Three miRNAs (miR-146a-5p, miR-122-5p and miR-21-5p) were identified using expression pattern analysis, and the levels were significantly decreased after acitretin treatment (<i>P</i>&lt; 0.001). Receiver operating characteristic (ROC) analyses indicated that the three miRNAs have the potential to be utilized as molecular markers to evaluate the therapeutic effect of acitretin, and the values of the area under the curve (AUC) were 0.825, 0.831, and 0.796, respectively. In addition, we predicted target genes of the three miRNAs and performed signaling pathway enrichment analyses. The results demonstrated that the target genes were mainly involved in the MAPK, JAK-STAT, and NF-κB signaling pathways, which were further validated through <i>in vitro</i> experiments. In conclusion, acitretin can suppress miRNA-mediated MAPK, JAK-STAT, and NF-κB signaling pathways by decreasing miRNAs expression, thereby inhibiting the proliferation and inflammatory response of keratinocytes.
DOI: 10.6084/m9.figshare.14577495.v1
title: Circulating microRNA profile unveils mechanisms of action of acitretin for psoriasis vulgaris

description: Psoriasis vulgaris is a common chronic and recurrent inflammatory skin disease. In clinical practice, acitretin is the first-line treatment drug for psoriasis vulgaris. MicroRNAs (miRNAs) play a vital role in the initiation and development of psoriasis vulgaris. However few studies focused on the mechanisms of acitretin in the treatment of psoriasis vulgaris from the perspective of miRNAs. Here, the expression profiles of circulating miRNAs in the plasma of 12 patients with psoriasis vulgaris before and after acitretin treatment were sequenced. Three miRNAs (miR-146a-5p, miR-122-5p and miR-21-5p) were identified using expression pattern analysis, and the levels were significantly decreased after acitretin treatment (<i>P</i>&lt; 0.001). Receiver operating characteristic (ROC) analyses indicated that the three miRNAs have the potential to be utilized as molecular markers to evaluate the therapeutic effect of acitretin, and the values of the area under the curve (AUC) were 0.825, 0.831, and 0.796, respectively. In addition, we predicted target genes of the three miRNAs and performed signaling pathway enrichment analyses. The results demonstrated that the target genes were mainly involved in the MAPK, JAK-STAT, and NF-κB signaling pathways, which were further validated through <i>in vitro</i> experiments. In conclusion, acitretin can suppress miRNA-mediated MAPK, JAK-STAT, and NF-κB signaling pathways by decreasing miRNAs expression, thereby inhibiting the proliferation and inflammatory response of keratinocytes.
DOI: 10.6084/m9.figshare.21393263
title: FADD phosphorylation contributes to development of renal fibrosis by accelerating epithelial-mesenchymal transition

description: FADD, a classical apoptotic signaling adaptor, has recently been reported to exhibit a series of non-apoptotic functions. Here, we report that FADD may play a critical role in the development of renal fibrosis. Neutrophil infiltration in the renal interstitial part, glomerular mesangial cell proliferation, and base-membrane thickening were observed in FADD-D mice by H&E, PAS, and PASM staining. Immunofluorescence analysis revealed that macrophage infiltration was significantly enhanced in FADD-D mice. Renal fibrosis might be induced by IgA nephritis in FADD-D mice as evidenced by increased Ki67 and type IV collagen. Additionally, the levels of α-SMA, Fibronectin, and Vimentin were also found to be elevated. Mechanism study indicated that the TLR4/myD88/NF-κB signaling pathway was activated in FADD-D mice. Moreover, FADD phosphorylation activated the mTOR and TGF-β/Smad pathway and accelerated the process of epithelial mesenchymal transition. Further studies indicated that the TGF-β1 pathway was also activated and the process of EMT was accelerated in both FADD-disrupted HEK293 cells and FADD-deficient MES cells. Thus, we concluded that FADD phosphorylation could lead to IgA nephritis and eventually result in renal fibrosis. Taken together, our study provides evidence, for the first time, that FADD, especially in its phosphorylated form, has an effect on the development of renal fibrosis. <b>Abbreviations:</b> FADD: FAS-associated protein with death domain; DED: death effector domain; DD: death domain; CKD: chronic kidney disease; ECM: extracellular matrix; ESRD: end-stage renal disease; RRT: renal replacement therapy; H&E: hematoxylin and eosin; PASM: periodic acid silver methenamine
DOI: 10.6084/m9.figshare.21393263.v1
title: FADD phosphorylation contributes to development of renal fibrosis by accelerating epithelial-mesenchymal transition

description: FADD, a classical apoptotic signaling adaptor, has recently been reported to exhibit a series of non-apoptotic functions. Here, we report that FADD may play a critical role in the development of renal fibrosis. Neutrophil infiltration in the renal interstitial part, glomerular mesangial cell proliferation, and base-membrane thickening were observed in FADD-D mice by H&E, PAS, and PASM staining. Immunofluorescence analysis revealed that macrophage infiltration was significantly enhanced in FADD-D mice. Renal fibrosis might be induced by IgA nephritis in FADD-D mice as evidenced by increased Ki67 and type IV collagen. Additionally, the levels of α-SMA, Fibronectin, and Vimentin were also found to be elevated. Mechanism study indicated that the TLR4/myD88/NF-κB signaling pathway was activated in FADD-D mice. Moreover, FADD phosphorylation activated the mTOR and TGF-β/Smad pathway and accelerated the process of epithelial mesenchymal transition. Further studies indicated that the TGF-β1 pathway was also activated and the process of EMT was accelerated in both FADD-disrupted HEK293 cells and FADD-deficient MES cells. Thus, we concluded that FADD phosphorylation could lead to IgA nephritis and eventually result in renal fibrosis. Taken together, our study provides evidence, for the first time, that FADD, especially in its phosphorylated form, has an effect on the development of renal fibrosis. <b>Abbreviations:</b> FADD: FAS-associated protein with death domain; DED: death effector domain; DD: death domain; CKD: chronic kidney disease; ECM: extracellular matrix; ESRD: end-stage renal disease; RRT: renal replacement therapy; H&E: hematoxylin and eosin; PASM: periodic acid silver methenamine
DOI: 10.6084/m9.figshare.14053239
title: Additional file 11 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 11 : Table S10. GO analysis of target genes of DElncRNAs predicted based on the sequence similarity.
DOI: 10.6084/m9.figshare.14053239.v1
title: Additional file 11 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 11 : Table S10. GO analysis of target genes of DElncRNAs predicted based on the sequence similarity.
DOI: 10.6084/m9.figshare.14053245
title: Additional file 1 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 1 : Table S1. Primers used for real-time quantitative PCR (RT-qPCR) experiment of lncRNAs.
DOI: 10.6084/m9.figshare.14053245.v1
title: Additional file 1 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 1 : Table S1. Primers used for real-time quantitative PCR (RT-qPCR) experiment of lncRNAs.
DOI: 10.6084/m9.figshare.14053233
title: Additional file 10 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 10 : Table S9. The list of target genes of DElncRNAs in liver and adrenal glands predicted based on the sequence similarity search method.
DOI: 10.6084/m9.figshare.14053233.v1
title: Additional file 10 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 10 : Table S9. The list of target genes of DElncRNAs in liver and adrenal glands predicted based on the sequence similarity search method.
DOI: 10.6084/m9.figshare.14053242
title: Additional file 12 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 12 : Table S11. GO analysis of target DEGs of DElncRNAs predicted based on the sequence similarity.
DOI: 10.6084/m9.figshare.21393282
title: Prevalence and molecular characterization of alpha and beta-Thalassemia mutations among Hakka people in southern China

description: Abstract Our aim was to investigate molecular features of thalassemia for proper clinical consultation and prevention in Heyuan. In our research, a total of 25,437 positive screening subjects were further subjected to a genetic analysis of α-thalassemia (α-thal) and β-thalassemia (β-thal). The deletion of α-thal mutation was tested by Gap-PCR, while the non-deletion of α-thal and β-thal mutation were identified by the PCR-reverse dot blot (PCR-RDB) technique. Nested PCR detected Hkαα/-- SEA and Hkαα/αα. Among the 25,437 positive screening subjects, 44.09% (11216/25437) subjects were bearers of thalassemia variations, and 30.85% (7847/25437) subjects showed α-thal changes alone. Among the 23 genotypes with α-thal mutation alone, the three common genotypes were --SEA/αα(68.34%), -α3.7/αα(16.44%), and -α4.2/αα(6.38%). Of the 11.50% (2924/25437) subjects and 29 genotypes with β-thal mutation alone, the three common genotypes were βCD41-42/βN(36.22%), βIVS-II-654/βN(30.88%), and β-28/βN(13.47%). Additionally, of the 1.75% (445/25437) subjects and 55 genotypes showed both α- and β-thal mutations. We also identified 269 cases of Hb H and six patients of Hkαα. Furthermore, the common genotypes of α-thal and β-thal mutations were consistent with allele frequencies of mutations. Our study establishes molecular features of thalassemia among Hakka people in Heyuan. It will be useful for developing strategies to prevent thalassemia.
DOI: 10.6084/m9.figshare.14053242.v1
title: Additional file 12 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 12 : Table S11. GO analysis of target DEGs of DElncRNAs predicted based on the sequence similarity.
DOI: 10.6084/m9.figshare.14053248
title: Additional file 2 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 2 : Table S2. Statistics summary of reads generated from 12 RNA-seq libraries in Control and H120 groups.
DOI: 10.6084/m9.figshare.21393282.v1
title: Prevalence and molecular characterization of alpha and beta-Thalassemia mutations among Hakka people in southern China

description: Abstract Our aim was to investigate molecular features of thalassemia for proper clinical consultation and prevention in Heyuan. In our research, a total of 25,437 positive screening subjects were further subjected to a genetic analysis of α-thalassemia (α-thal) and β-thalassemia (β-thal). The deletion of α-thal mutation was tested by Gap-PCR, while the non-deletion of α-thal and β-thal mutation were identified by the PCR-reverse dot blot (PCR-RDB) technique. Nested PCR detected Hkαα/-- SEA and Hkαα/αα. Among the 25,437 positive screening subjects, 44.09% (11216/25437) subjects were bearers of thalassemia variations, and 30.85% (7847/25437) subjects showed α-thal changes alone. Among the 23 genotypes with α-thal mutation alone, the three common genotypes were --SEA/αα(68.34%), -α3.7/αα(16.44%), and -α4.2/αα(6.38%). Of the 11.50% (2924/25437) subjects and 29 genotypes with β-thal mutation alone, the three common genotypes were βCD41-42/βN(36.22%), βIVS-II-654/βN(30.88%), and β-28/βN(13.47%). Additionally, of the 1.75% (445/25437) subjects and 55 genotypes showed both α- and β-thal mutations. We also identified 269 cases of Hb H and six patients of Hkαα. Furthermore, the common genotypes of α-thal and β-thal mutations were consistent with allele frequencies of mutations. Our study establishes molecular features of thalassemia among Hakka people in Heyuan. It will be useful for developing strategies to prevent thalassemia.
DOI: 10.6084/m9.figshare.14053248.v1
title: Additional file 2 of Genome-wide identification and functional prediction of long non-coding RNAs in Sprague-Dawley rats during heat stress

description: Additional file 2 : Table S2. Statistics summary of reads generated from 12 RNA-seq libraries in Control and H120 groups.