cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7676558
title: Overexpression of salt-induced protein (salT) delays leaf senescence in rice

description: Abstract Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gene affecting the leaf senescence induced by natural and dark conditions.
DOI: 10.6084/m9.figshare.14490412
title: Additional file 1 of The evolution of opsin genes in five species of mirid bugs: duplication of long-wavelength opsins and loss of blue-sensitive opsins

description: Additional file 1: Table S1. Contigs showing high identity with opsins. Table S2: Primers used in this study.
DOI: 10.6084/m9.figshare.14490412.v1
title: Additional file 1 of The evolution of opsin genes in five species of mirid bugs: duplication of long-wavelength opsins and loss of blue-sensitive opsins

description: Additional file 1: Table S1. Contigs showing high identity with opsins. Table S2: Primers used in this study.
DOI: 10.6084/m9.figshare.14490415.v1
title: Additional file 2 of The evolution of opsin genes in five species of mirid bugs: duplication of long-wavelength opsins and loss of blue-sensitive opsins

description: Additional file 2. Sequences used for phylogenetic and selection analyses.
DOI: 10.6084/m9.figshare.11870781.v1
title: Additional file 11 of Single-nucleus RNA-seq identifies Huntington disease astrocyte states

description: Additional file 11. Differential correlation analysis between astrocytic genes in HD and control
DOI: 10.6084/m9.figshare.7676777
title: Polyhedral Oligomeric Silsesquioxane (POSS) as Reinforcing Agent for Waterborne Polyurethane Coatings on Wood

description: Polyhedral oligomeric silsesquioxane (POSS) was added as a reinforcing agent in waterborne polyurethane (WPU)-based coatings to improve their properties. The morphology, structure, thermal stability as well as mechanical properties of the resulting WPU and WPU/POSS hybrid films were investigated. The good compatibility of POSS in the WPU matrices was demonstrated by transmission electron microscopy. Furthermore, Fourier-transform infrared spectroscopy analysis (FTIR) suggested the successful bonding of POSS and WPU matrices. The thermal stability of WPU/POSS hybrids was improved than that of pure WPU according to thermal gravimetric analysis (TGA). The results also revealed the enhancement of the pencil hardness and abrasion resistance of the hybrid films compared with WPU. However, the pull-off adhesion slightly decreased from Grade 0 to Grade 2.
DOI: 10.6084/m9.figshare.11870814.v1
title: Additional file 16 of Single-nucleus RNA-seq identifies Huntington disease astrocyte states

description: Additional file 16. Differential gene expression between control and HD neuronal nuclei, GO term enriched in top differentially upregulated and downregualted genes.
DOI: 10.6084/m9.figshare.11870832
title: Additional file 2 of Single-nucleus RNA-seq identifies Huntington disease astrocyte states

description: Additional file 2. Genes used in gene set enrichment analysis [10], in cell classifier, and discovered cell-type marker genes based on single nuclei RNAseq data
DOI: 10.6084/m9.figshare.21308664.v1
title: Additional file 1 of Functional analysis revealed the involvement of ZmABCB15 in resistance to rice black-streaked dwarf virus infection

description: Additional file 1: Table S1. The disease rates of the five varieties after inoculating RBSDV.
DOI: 10.6084/m9.figshare.11870823.v1
title: Additional file 17 of Single-nucleus RNA-seq identifies Huntington disease astrocyte states

description: Additional file 17. Microglial genes shown in heatmap of figure S6A
DOI: 10.6084/m9.figshare.11870844
title: Additional file 4 of Single-nucleus RNA-seq identifies Huntington disease astrocyte states

description: Additional file 4. Supplementary Data. (1) Raw counts and RPKM counts of Bulk RNAseq data. (2)Results of differential gene expression analysis of each astrocytic cluster against all other clusters.
DOI: 10.6084/m9.figshare.11871063.v1
title: The associations of <i>CYP19A1</i> rs700518 polymorphism with bone mineral density and risk of osteoporosis: a meta-analysis

description: Osteoporosis is now a worldwide public health problem that seriously endangers human health, but its causes have not yet been fully clarified. Recently, increasing evidence suggested that polymorphisms in <i>CYP19A1</i> gene were associated with osteoporosis risk and bone mineral density (BMD), but results remained conflicting. We herein performed a meta-analysis based on evidence currently available from the literature to make a more precise estimation of these relationships. The PubMed, Embase, Cochrane library, CNKI (China National Knowledge Infrastructure), and Wan Fang databases were searched for eligible studies. Odds ratio (OR), mean difference (MD), and 95% confidence interval (CI) were applied to assess the strength of these relationships. A total of 8 studies involving 2632 subjects were included in our meta-analysis. We observed that the AG genotype of <i>CYP19A1</i> rs700518 was significantly associated with lower BMD values of lumbar spine and femoral neck (AG vs. GG: <i>p</i> = .001 and.01, respectively). However, this polymorphism had no obvious impacts on osteoporosis risk according to current available data. In conclusion, the present meta-analysis showed that <i>CYP19A1</i> rs700518 polymorphism may be a potential candidate biomarker for osteoporosis screening, early diagnosis, and treatment, which will help improve individualized therapy of osteoporosis patients in clinics.
DOI: 10.6084/m9.figshare.5579788
title: Role of GABA<sub>B</sub> receptors and p38MAPK/NF-κB pathway in paclitaxel-induced apoptosis of hippocampal neurons

description: <b>Context:</b> The effects of the anticancer drug paclitaxel on learning and memory are rarely studied. <b>Objective:</b> This study investigated changes in GABA<sub>B</sub> receptor expression during paclitaxel-induced apoptosis of hippocampal neurons and the role of the p38MAPK/NF-κB pathway in this process. <b>Materials and methods:</b> Hippocampal neurons isolated from neonatal Sprague–Dawley rats were divided into six groups: Control (C), SB (10 µL of 10-µmol/L SB203580), SN (53 µg/mL SN50), N (1 µmol/L paclitaxel), SB + N (10 µmol/L SB203580 + 1 µmol/L paclitaxel) and SN + N (53 µg/mL SN50 + 1 µmol/L paclitaxel). Cells in different groups were treated with corresponding agents for 24 h at 37 °C. The apoptosis rate and protein levels of GABA<sub>B1</sub> receptors and NF-κB p65 were evaluated. Rat models of neuropathic pain was induced by paclitaxel and were divided into four groups such as N, B + N, SN + N and SN + B + N groups. Rats in the N group received intrathecal injections of normal saline solution. Rats in the B + N group received intrathecal injections of 10 μL baclofen (0.05 μg/μL). Rats in the SN + N and SN + B + N groups received intrathecal injections of SN50 and SN50 plus baclofen, respectively. Spatial learning and memory were evaluated in rat models based on the escape latency and the number of crossings over the platform and protein levels of GABA<sub>B1</sub> receptors, NF-κB, IL-1β and TNFα were measured by immunohistochemistry assay and western blot. <b>Results:</b> The neuronal apoptosis rate was significantly increased in N (49.16 ± 3.12)%, SB + N (31.18 ± 3.02)% and SN + N (28.47 ± 3.75)% groups, accompanied by increased levels of GABA<sub>B1</sub> receptors and NF-κB p65 (<i>p</i> &lt; 0.05). The paclitaxel-treated rats demonstrated significantly increased latency (24.32 ± 2.94)s and decreased the crossings number (3.14 ± 0.63) after 15 d in the Morris water maze (<i>p</i> &lt; 0.05). Immunohistochemistry assay showed that compared with the N group (GABA<sub>B1:</sub>9.0 ± 1.6, NF-κB p65:29.6 ± 2.4, IL-1β: 30.4 ± 3.4, TNFα: 31.0 ± 3.4), B + N, SN + N and SN + B + N groups evidently increased levels of GABA<sub>B1</sub> receptor (B + N:SN + N:SN + B + N = 19.4 ± 2.1:20.8 ± 1.9:28.0 ± 1.9) but significantly decreased levels of NF-κB p65 (B + N:SN + N:SN + B + N = 21.2 ± 1.5:18.6 ± 2.1:12.6 ± 1.5), IL-1β (B + N:SN + N:SN + B + N = 22.0 ± 1.0:19.6 ± 1.8:14.6 ± 1.5) and TNF α (B + N:SN + N:SN + B + N = 23.0 ± 1.6:22.2 ± 0.8:16.6 ± 1.7). Similar findings were found in western blot analysis. <b>Discussions and conclusions:</b> Paclitaxel may reduce cognitive function in rats through the p38MAPK/NF-κB pathway and GABA<sub>B1</sub> receptors.
DOI: 10.6084/m9.figshare.6627974.v1
title: MOESM3 of Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48Â hours post-infection through RNA-seq

description: Additional file 3. Differentially expressed genes in the uninfected and 12Â hpi duckling livers. The list of all differentially expressed genes in the livers of ducklings in the control group and 12Â hpi group.
DOI: 10.6084/m9.figshare.7676558.v1
title: Overexpression of salt-induced protein (salT) delays leaf senescence in rice

description: Abstract Senescence, a highly programmed process, largely determines yield and quality of crops. However, knowledge about the onset and progression of leaf senescence in crop plants is still limited. Here, we report that salt-induced protein (salT), a new gene, may be involved in leaf senescence. Overexpressing salT could prolong the duration of leaves with higher concentrations of chlorophyll compared with the wild type. Moreover, overexpression of salT could delay the senescence of rice leaves though the inhibition of senescence associated genes (SAGs). Overall, the characterization of salT suggested that it is a new gene affecting the leaf senescence induced by natural and dark conditions.
DOI: 10.6084/m9.figshare.11870865
title: Additional file 9 of Single-nucleus RNA-seq identifies Huntington disease astrocyte states

description: Additional file 9. Differential gene expression between control and HD Astrocytic nuclei, GO term enriched in top differentially upregulated and downregulated genes
DOI: 10.6084/m9.figshare.6627992.v1
title: MOESM4 of Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48Â hours post-infection through RNA-seq

description: Additional file 4. Differentially expressed genes in the uninfected and 48Â hpi duckling livers. The list of all differentially expressed genes in the livers of ducklings in the control group and 48Â hpi group.
DOI: 10.6084/m9.figshare.6628001.v1
title: MOESM5 of Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48Â hours post-infection through RNA-seq

description: Additional file 5. Genes expressed only in the livers of ducklings at 12Â hpi. Compared with the control group, genes expressed only in the livers of ducklings at 12Â hpi.
DOI: 10.6084/m9.figshare.19211444.v1
title: Additional file 4 of Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers

description: Additional file 3: Table S3. Differential test results for CRC vs CRA.
DOI: 10.6084/m9.figshare.11871150.v1
title: Lipophagy-derived fatty acids undergo extracellular efflux via lysosomal exocytosis

description: The autophagic degradation of lipid droplets (LDs), termed lipophagy, is a major mechanism that contributes to lipid turnover in numerous cell types. While numerous factors, including nutrient deprivation or overexpression of PNPLA2/ATGL (patatin-like phospholipase domain containing 2) drive lipophagy, the trafficking of fatty acids (FAs) produced from this pathway is largely unknown. Herein, we show that PNPLA2 and nutrient deprivation promoted the extracellular efflux of FAs. Inhibition of autophagy or lysosomal lipid degradation attenuated FA efflux highlighting a critical role for lipophagy in this process. Rather than direct transport of FAs across the lysosomal membrane, lipophagy-derived FA efflux requires lysosomal fusion to the plasma membrane. The lysosomal Ca2+ channel protein MCOLN1/TRPML1 (mucolipin 1) regulates lysosomal-plasma membrane fusion and its overexpression increased, while inhibition blocked FA efflux. In addition, inhibition of autophagy/lipophagy or MCOLN1, or sequestration of extracellular FAs with BSA attenuated the oxidation and re-esterification of lipophagy-derived FAs. Overall, these studies show that the well-established pathway of lysosomal fusion to the plasma membrane is the primary route for the disposal of FAs derived from lipophagy. Moreover, the efflux of FAs and their reuptake or subsequent extracellular trafficking to adjacent cells may play an important role in cell-to-cell lipid exchange and signaling. <b>Abbreviations:</b> ACTB: beta actin; ADRA1A: adrenergic receptor alpha, 1a; ALB: albumin; ATG5: autophagy related 5; ATG7: autophagy related 7; BafA1: bafilomycin A1; BECN1: beclin 1; BHBA: beta-hydroxybutyrate; BSA: bovine serum albumin; CDH1: e-cadherin; CQ: chloroquine; CTSB: cathepsin B; DGAT: diacylglycerol O-acyltransferase; FA: fatty acid; HFD: high-fat diet; LAMP1: lysosomal-associated membrane protein 1; LD: lipid droplet; LIPA/LAL: lysosomal acid lipase A; LLME: Leu-Leu methyl ester hydrobromide; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MCOLN1/TRPML1: mucolipin 1; MEF: mouse embryo fibroblast; PBS: phosphate-buffered saline; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PLIN: perilipin; PNPLA2/ATGL patatin-like phospholipase domain containing 2; RUBCN (rubicon autophagy regulator); SM: sphingomyelin; TAG: triacylglycerol; TMEM192: transmembrane protein 192; VLDL: very low density lipoprotein.
DOI: 10.6084/m9.figshare.6628058
title: MOESM9 of Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48Â hours post-infection through RNA-seq

description: Additional file 9. GO annotation information of genes in the livers of ducklings at 12Â hpi.
DOI: 10.6084/m9.figshare.19211447
title: Additional file 5 of Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers

description: Additional file 4: Table S4. The list of significant associations among metabolites and bacteria following direct trends.
DOI: 10.6084/m9.figshare.6628058.v1
title: MOESM9 of Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48Â hours post-infection through RNA-seq

description: Additional file 9. GO annotation information of genes in the livers of ducklings at 12Â hpi.
DOI: 10.6084/m9.figshare.19211447.v1
title: Additional file 5 of Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers

description: Additional file 4: Table S4. The list of significant associations among metabolites and bacteria following direct trends.
DOI: 10.6084/m9.figshare.7677077.v1
title: Increased expression levels of Syntaxin 1A and Synaptobrevin 2/Vesicle-Associated Membrane Protein-2 are associated with the progression of bladder cancer

description: Abstract Gene expression is tightly regulated in time and space through a multitude of factors consisting of signaling molecules. Soluble N-ethylmaleimide-sensitive-factor attachment protein receptors (SNARE) are membrane proteins responsible for the intercellular trafficking of signals through endocytosis and exocytosis of vesicles. Altered expression of SNARE proteins in cellular communication is the major hallmark of cancer phenotypes as indicated in recent studies. SNAREs play an important role in maintaining cell growth and epithelial membrane permeability of the bladder and are not only involved in cancer progression but also metastatic cell invasion through SNARE-mediated trafficking. Synaptobrevin2/Vesicle associated membrane protein-2 (v-SNARE) and Syntaxin (t-SNARE) form a vesicular docking complex during endocytosis. Some earlier studies have shown a critical role of SNARE in colon, lungs, and breast cancer progression and metastasis. In this study, we analyzed the relative expression of the STX1A and VAMP2 (SYB2) for their possible association in the progression and metastasis of bladder cancer. The profiling of the genes showed a significant increase in STX1A and VAMP2 expression (p &lt; 0.001) in high-grade tumor cells compared to normal and low-grade tumors. These findings suggest that elevated expression of STX1A and VAMP2 might have caused the abnormal progression and invasion of cancer cells leading to the transformation of cells into high-grade tumor in bladder cancer.
DOI: 10.6084/m9.figshare.19211441
title: Additional file 3 of Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers

description: Additional file 2: Table S2. Differential test results for CRC vs NC.
DOI: 10.6084/m9.figshare.7676870.v1
title: The effects of high-flow nasal cannula on intubation and re-intubation in critically ill patients: a systematic review, meta-analysis and trial sequential analysis

description: ABSTRACT Objective: To evaluate the efficacy of high-flow nasal cannula in the prevention of intubation and re-intubation in critically ill patients compared to conventional oxygen therapy or noninvasive ventilation. Methods: This systematic review was performed through an electronic database search of articles published from 1966 to April 2018. The primary outcome was the need for intubation or re-intubation. The secondary outcomes were therapy escalation, mortality at the longest follow-up, hospital mortality and the need for noninvasive ventilation. Results: Seventeen studies involving 3,978 patients were included. There was no reduction in the need for intubation or re-intubation with high-flow nasal cannula (OR 0.72; 95%CI 0.52 - 1.01; p = 0.056). There was no difference in the need for therapy escalation (OR 0.80, 95% CI 0.59 - 1.08, p = 0.144), mortality at the longest follow-up (OR 0.94; 95%CI 0.70 - 1.25; p = 0.667), hospital mortality (OR 0.84; 95%CI 0.56 - 1.26; p = 0.391) or noninvasive ventilation (OR 0.64, 95%CI 0.39 - 1.05, p = 0.075). In the trial sequential analysis, the number of events included was lower than the optimal information size with a global type I error &gt; 0.05. Conclusion: In the present study and setting, high-flow nasal cannula was not associated with a reduction of the need for intubation or re-intubation in critically ill patients.
DOI: 10.6084/m9.figshare.11871063
title: The associations of <i>CYP19A1</i> rs700518 polymorphism with bone mineral density and risk of osteoporosis: a meta-analysis

description: Osteoporosis is now a worldwide public health problem that seriously endangers human health, but its causes have not yet been fully clarified. Recently, increasing evidence suggested that polymorphisms in <i>CYP19A1</i> gene were associated with osteoporosis risk and bone mineral density (BMD), but results remained conflicting. We herein performed a meta-analysis based on evidence currently available from the literature to make a more precise estimation of these relationships. The PubMed, Embase, Cochrane library, CNKI (China National Knowledge Infrastructure), and Wan Fang databases were searched for eligible studies. Odds ratio (OR), mean difference (MD), and 95% confidence interval (CI) were applied to assess the strength of these relationships. A total of 8 studies involving 2632 subjects were included in our meta-analysis. We observed that the AG genotype of <i>CYP19A1</i> rs700518 was significantly associated with lower BMD values of lumbar spine and femoral neck (AG vs. GG: <i>p</i> = .001 and.01, respectively). However, this polymorphism had no obvious impacts on osteoporosis risk according to current available data. In conclusion, the present meta-analysis showed that <i>CYP19A1</i> rs700518 polymorphism may be a potential candidate biomarker for osteoporosis screening, early diagnosis, and treatment, which will help improve individualized therapy of osteoporosis patients in clinics.
DOI: 10.6084/m9.figshare.21308664
title: Additional file 1 of Functional analysis revealed the involvement of ZmABCB15 in resistance to rice black-streaked dwarf virus infection

description: Additional file 1: Table S1. The disease rates of the five varieties after inoculating RBSDV.
DOI: 10.6084/m9.figshare.11871150
title: Lipophagy-derived fatty acids undergo extracellular efflux via lysosomal exocytosis

description: The autophagic degradation of lipid droplets (LDs), termed lipophagy, is a major mechanism that contributes to lipid turnover in numerous cell types. While numerous factors, including nutrient deprivation or overexpression of PNPLA2/ATGL (patatin-like phospholipase domain containing 2) drive lipophagy, the trafficking of fatty acids (FAs) produced from this pathway is largely unknown. Herein, we show that PNPLA2 and nutrient deprivation promoted the extracellular efflux of FAs. Inhibition of autophagy or lysosomal lipid degradation attenuated FA efflux highlighting a critical role for lipophagy in this process. Rather than direct transport of FAs across the lysosomal membrane, lipophagy-derived FA efflux requires lysosomal fusion to the plasma membrane. The lysosomal Ca2+ channel protein MCOLN1/TRPML1 (mucolipin 1) regulates lysosomal-plasma membrane fusion and its overexpression increased, while inhibition blocked FA efflux. In addition, inhibition of autophagy/lipophagy or MCOLN1, or sequestration of extracellular FAs with BSA attenuated the oxidation and re-esterification of lipophagy-derived FAs. Overall, these studies show that the well-established pathway of lysosomal fusion to the plasma membrane is the primary route for the disposal of FAs derived from lipophagy. Moreover, the efflux of FAs and their reuptake or subsequent extracellular trafficking to adjacent cells may play an important role in cell-to-cell lipid exchange and signaling. <b>Abbreviations:</b> ACTB: beta actin; ADRA1A: adrenergic receptor alpha, 1a; ALB: albumin; ATG5: autophagy related 5; ATG7: autophagy related 7; BafA1: bafilomycin A1; BECN1: beclin 1; BHBA: beta-hydroxybutyrate; BSA: bovine serum albumin; CDH1: e-cadherin; CQ: chloroquine; CTSB: cathepsin B; DGAT: diacylglycerol O-acyltransferase; FA: fatty acid; HFD: high-fat diet; LAMP1: lysosomal-associated membrane protein 1; LD: lipid droplet; LIPA/LAL: lysosomal acid lipase A; LLME: Leu-Leu methyl ester hydrobromide; MAP1LC3B/LC3: microtubule associated protein 1 light chain 3 beta; MCOLN1/TRPML1: mucolipin 1; MEF: mouse embryo fibroblast; PBS: phosphate-buffered saline; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PLIN: perilipin; PNPLA2/ATGL patatin-like phospholipase domain containing 2; RUBCN (rubicon autophagy regulator); SM: sphingomyelin; TAG: triacylglycerol; TMEM192: transmembrane protein 192; VLDL: very low density lipoprotein.