cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14275661.v1
title: Impact of different clear corneal incision sizes on anterior corneal aberration for cataract surgery

description: ABSTRACT Purpose: To investigate the impact of different sizes of steep meridian clear corneal incisions for phacoemul sification on anterior corneal higher-order aberrations. Methods: Medical records of patients who underwent 2.2-mm coaxial micro-incision cataract surgery or 2.75-mm coaxial small-incision cataract surgery were retrospectively reviewed. Only patients with preexisting anterior corneal astigmatism &lt;2.00 diopters (D) and ≥0.50 D who underwent a steep meridian clear corneal incision were included. Primary outcomes were 3rd- to 6th-order anterior corneal higher-order aberrations with an 8-mm pupil. Anterior corneal astigmatism and effective phaco time were evaluated as secondary outcomes. Preoperative and 3-month postoperative outcomes were evaluated. Results: Anterior corneal astigmatism significantly decreased after both procedures; however, there was no significant difference found in surgically induced anterior corneal astigmatism between the two procedures (p=0.146). Although the total higher-order aberrations did not significantly change after both procedures, the group comparison showed a significant difference in surgically induced total higher-order aberrations (a decrease of 0.337 ± 1.156 mm in 2.2-mm coaxial micro-incision cataract surgery and an increase of 0.106 ± 0.521 mm in 2.75-mm coaxial small-incision cataract surgery, p=0.046). Spherical aberrations significantly decreased after 2.2-mm coaxial micro-incision cataract surgery (p=0.001), whereas they did not change significantly after 2.75-mm coaxial small-incision cataract surgery (p=0.564). Coma did not significantly change after either of the procedures. Trefoil did not significantly change after 2.2-mm coaxial micro-incision cataract surgery (p=0.361), whereas it significantly increased after 2.75-mm coaxial small-incision cataract surgery (p&lt;0.001). There was no significant difference shown in effective phaco time between the procedures. A significantly positive correlation was shown between surgically induced anterior corneal astigmatism and coma in 2.75-mm coaxial small-incision cataract surgery (r=0.387, p=0.006). There was no significant correlation found between any surgically induced higher-order aberration changes and effective phaco time. Conclusions: The results showed that 2.2-mm coaxial micro-incision cataract surgery and 2.75-mm coaxial small-incision cataract surgery did not significantly degrade the total higher-order aberrations of the anterior cornea. However, the surgically induced changes in total higher-order aberration showed a significant difference between the two procedures, with a slight reduction after 2.2-mm coaxial micro-incision cataract surgery and a slight increase after 2.75-mm coaxial small-incision cataract surgery. Phaco time and power used during surgery had no impact on corneal aberrations.
DOI: 10.6084/m9.figshare.16897043
title: N6-methyladenosine reader YTH N6-methyladenosine RNA binding protein 3 or insulin like growth factor 2 mRNA binding protein 2 knockdown protects human bronchial epithelial cells from hypoxia/reoxygenation injury by inactivating p38 MAPK, AKT, ERK1/2, and NF-κB pathways

description: Lung ischemia/reperfusion (I/R) injury (LIRI) is a common complication after lung transplantation, embolism, and trauma. N6-methyladenosine (m6A) methylation modification is implicated in the pathogenesis of I/R injury. However, there are no or few reports of m6A-related regulators in LIRI till now. In this text, dysregulated genes in lung tissues of LIRI rats versus the sham group were identified by RNA sequencing (RNA-seq). RNA-seq outcomes revealed that only YTH N6-methyladenosine RNA binding protein 3 (YTHDF3) and insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) were differentially expressed in the LIRI versus sham group among 20 m6A-related regulators. Next, the functions and molecular mechanisms of YTHDF3 and IGF2BP2 in LIRI were investigated in a hypoxia/reoxygenation-induced BEAS-2B cell injury model <i>in vitro</i>. Results showed that YTHDF3 or IGF2BP2 knockdown attenuated hypoxia/reoxygenation-mediated inhibitory effects on cell survival and cell cycle progression and inhibited hypoxia/reoxygenation-induced cell apoptosis and pro-inflammatory cytokine secretion in BEAS-2B cells. Genes that could be directly regulated by YTHDF3 or IGF2BP2 were identified based on prior experimental data and bioinformatics analysis. Moreover, multiple potential downstream pathways of YTHDF3 and IGF2BP2 were identified by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis of the above-mentioned genes. Among these potential pathways, we demonstrated that YTHDF3 or IGF2BP2 knockdown inhibited hypoxia/reoxygenation-activated p38, ERK1/2, AKT, and NF-κB pathways in BEAS-2B cells. In conclusion, YTHDF3 or IGF2BP2 knockdown weakened hypoxia/reoxygenation-induced human lung bronchial epithelial cell injury by inactivating p38, AKT, ERK1/2, and NF-κB pathways.
DOI: 10.6084/m9.figshare.19518422.v1
title: Additional file 1 of Clinical implementation of RNA sequencing for Mendelian disease diagnostics

description: Additional file 1: Table S1. Sample annotation. Table S2. Extended summary of RNA-seq diagnosed cases. Table S3. Summary of candidate genes pinpointed via RNA-seq. Table S4. Summary of WES-diagnosed cases with an RNA-defect. Table S5. Recalled expression outliers at different mean and dispersion.
DOI: 10.6084/m9.figshare.7459859
title: MOESM5 of Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs

description: Additional file 5. Regulators of differentially expressed genes. Full list of regulators of differentially expressed genes.
DOI: 10.6084/m9.figshare.16897171
title: Data.zip

description: data and images
DOI: 10.6084/m9.figshare.19518464
title: Additional file 2 of Dynamic contrast-enhanced MRI radiomics nomogram for predicting axillary lymph node metastasis in breast cancer

description: Additional file 2.
DOI: 10.6084/m9.figshare.19518593
title: Additional file 4 of TMT-based proteomic analysis reveals integrins involved in the synergistic infection of reticuloendotheliosis virus and avian leukosis virus subgroup J

description: Additional file 4: Table S2. The significant differentially expressed proteins were identified by comparing co-infection with both viruses and infection with ALV-J only.
DOI: 10.6084/m9.figshare.7460021
title: Additional file 3: of Detecting the priority areas for health workforce allocation with LISA functions: an empirical analysis for China

description: Table S2. The number of different types of health workforce and population data in rural China in 2016. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460021.v1
title: Additional file 3: of Detecting the priority areas for health workforce allocation with LISA functions: an empirical analysis for China

description: Table S2. The number of different types of health workforce and population data in rural China in 2016. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460012.v1
title: Additional file 2: of Detecting the priority areas for health workforce allocation with LISA functions: an empirical analysis for China

description: Table S1. The number of different types of health workforce and population data in urban China in 2016. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460015
title: Additional file 10: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

description: Table S6. Organization of cis-acting regulatory elements in the promoters of subfamily II members of cotton GH3 gene family. The number represents the upstream distance to start codon. “+” and “-” represent the plus strand and minus strand, respectively. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.7460015.v1
title: Additional file 10: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

description: Table S6. Organization of cis-acting regulatory elements in the promoters of subfamily II members of cotton GH3 gene family. The number represents the upstream distance to start codon. “+” and “-” represent the plus strand and minus strand, respectively. (XLSX 84 kb)
DOI: 10.6084/m9.figshare.14275731.v1
title: High glucose induces pyroptosis of retinal microglia through NLPR3 inflammasome signaling

description: ABSTRACT Purpose: Diabetic retinopathy is currently considered a chronic inflammatory disease involving NOD-like receptor family pyrin domain containing 3 inflammasome activation and retinal microglial pyroptosis. In this study, we aimed to investigate whether NOD-like receptor family pyrin domain containing 3 inflammasome signaling induces pyroptotic death of retinal microglia under high-glucose conditions. Methods: Retinal microglia were stimulated by high glucose levels for 24 h. Cell viability, lactate dehydrogenase release, and caspase-1 activity were detected in vitro. The expression of pro-inflammatory cytokine (interleukin-1β, activated microglia marker ionized calcium-binding adapter molecule-1), NOD-like receptor family pyrin domain containing 3, cleaved caspase-1, and cleaved gasdermin D were examined. Subsequently, retinal microglia were pretreated with the inhibitors of NOD-like receptor family pyrin domain containing 3 inflammasome signaling prior to stimulation with high glucose, and their molecular and functional changes were evaluated. Results: High-glucose (25, 50, or 100 mM) stimulation decreased cell viability, but enhanced lactate dehydrogenase release and caspase-1 activity in a dose-dependent manner. Moreover, high glucose upregulated the protein expression of interleukin-1β, ionized calcium-binding adapter molecule-1, NOD-like receptor family pyrin domain containing 3, cleaved caspase-1, and cleaved gasdermin D. However, pretreatment with the inhibitors of NOD-like receptor family pyrin domain containing 3 inflammasome signaling inhibited high glucose (25 mM)-induced cytotoxicity, NOD-like receptor family pyrin domain containing 3 inflammasome activation, and pyroptosis of retinal microglia. Conclusions: NOD-like receptor family pyrin domain containing 3 inflammasome signaling may modulate retinal microglia-related inflammation and pyroptosis under high-glucose conditions.
DOI: 10.6084/m9.figshare.7460033.v1
title: Additional file 4: of Detecting the priority areas for health workforce allocation with LISA functions: an empirical analysis for China

description: Table S1. The density of different types of urban and rural health workforce in China in 2016. (XLSX 12â kb)
DOI: 10.6084/m9.figshare.7460033
title: Additional file 4: of Detecting the priority areas for health workforce allocation with LISA functions: an empirical analysis for China

description: Table S1. The density of different types of urban and rural health workforce in China in 2016. (XLSX 12â kb)
DOI: 10.6084/m9.figshare.7459877
title: MOESM7 of Regulators of Salmonella-host interaction identified by peripheral blood transcriptome profiling: roles of TGFB1 and TRP53 in intracellular Salmonella replication in pigs

description: Additional file 7. Real-time PCR result. Raw data and statistical results for real-time PCR.
DOI: 10.6084/m9.figshare.14275803
title: Fluorofenidone inhibits epithelial-mesenchymal transition in human lens epithelial cell line FHL 124: a promising therapeutic strategy against posterior capsular opacification

description: ABSTRACT Purpose: The present study aimed to investigate the inhibitory effect of fluorofenidone against transforming growth factor β2-induced proliferation and epithelial-mesenchymal transition in human lens epithelial cell line FHL 124 and its potential mechanism. Methods: We evaluated the effect of fluorofenidone on proliferation and epithelial-mesenchymal transition of human lens epithelial cell line FHL 124 in vitro. After treatment with 0, 0.1, 0.2, 0.4, 0.6, and 1.0 mg/mL fluorofenidone, cell proliferation was measured via MTT assay. Cell viability was evaluated by lactate dehydrogenase activity from damaged cells. FHL 124 cells were treated with different transforming growth factor β2 concentrations (0-10 ng/mL) for 24 h and the expression of CTGF, α-SMA, COL-I, E-cadherin, and Fn were detected via quantitative polymerase chain reaction and Western blot analysis. After treatment with 0, 0.2, and 0.4 mg/ml fluorofenidone, the expressions of transforming growth factor β2 and SMADs were detected with real-time polymerase chain reaction and Western blot analysis. Expressions of CTGF, α-SMA, COL-I, and Fn were analyzed by immunocytochemistry assay. Results: The viability of FHL 124 cells was not inhibited when the fluorofenidone concentration was ≤0.4 mg/mL after the 24h treatment. Cytotoxicity was not detected via lactate dehydrogenase assay after the 24h and 36h treatment with 0.2 and 0.4 mg/mL fluorofenidone. Transforming growth factor β2 increased mRNA and protein expression of CTGF, α-SMA, COL-I, and Fn. However, fluorofenidone significantly suppressed expression of SMADs, CTGF, α-SMA, COL-I, and Fn in the absence or presence of transforming growth factor β2 stimulation. Conclusions: Fluorofenidone significantly inhibited expression of SMADs, CTGF, α-SMA, COL-I, and Fn in FHL 124 cells. Due to noncompliance in infants, fluorofenidone may become a novel therapeutic drug against posterior capsular opacification in infants.
DOI: 10.6084/m9.figshare.7460042.v1
title: Additional file 1: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

description: Table S1. All protein sequences used in this study. (XLSX 71â kb)
DOI: 10.6084/m9.figshare.7460132.v1
title: Additional file 4: of Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing

description: Table S1. Markers used for mapping. (XLS 3199 kb)
DOI: 10.6084/m9.figshare.7460096
title: Additional file 9: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

description: Table S5. The original RNA-seq data for GhGH3 expression pattern analysis. (XLSX 20â kb)
DOI: 10.6084/m9.figshare.13227312.v3
title: A VASt-domain protein regulates autophagy, membrane tension, and sterol homeostasis in rice blast fungus

description: Sterols are a class of lipids critical for fundamental biological processes and membrane dynamics. These molecules are synthesized in the endoplasmic reticulum (ER) and are transported bi-directionally between the ER and plasma membrane (PM). However, the trafficking mechanism of sterols and their relationship with macroautophagy/autophagy are still poorly understood in the rice blast fungus <i>Magnaporthe oryzae</i>. Here, we identified the VAD1 Analog of StAR-related lipid transfer (VASt) domain-containing protein MoVast1 via co-immunoprecipitation in <i>M. oryzae</i>. Loss of <i>MoVAST1</i> resulted in conidial defects, impaired appressorium development, and reduced pathogenicity. The MoTor (target of rapamycin in <i>M. oryzae</i>) activity is inhibited because MoVast1 deletion leads to high levels of sterol accumulation in the PM. Site-directed mutagenesis showed that the 902 T site is essential for localization and function of MoVast1. Through filipin or Flipper-TR staining, autophagic flux detection, MoAtg8 lipidation, and drug sensitivity assays, we uncovered that MoVast1 acts as a novel autophagy inhibition factor that monitors tension in the PM by regulating the sterol content, which in turn modulates the activity of MoTor. Lipidomics and transcriptomics analyses further confirmed that MoVast1 is an important regulator of lipid metabolism and the autophagy pathway. Our results revealed and characterized a novel sterol transfer protein important for <i>M. oryzae</i> pathogenicity. <b>Abbreviations:</b> AmB: amphotericin B; ATMT: <i>Agrobacterium tumefaciens</i>-mediated transformation; CM: complete medium; dpi: days post-inoculation; ER: endoplasmic reticulum; Flipper-TR: fluorescent lipid tension reporter; GO: Gene ontology; hpi: hours post-inoculation; IH: invasive hyphae; KEGG: kyoto encyclopedia of genes and genomes; MoTor: target of rapamycin in <i>Magnaporthe oryzae</i>; PalmC: palmitoylcarnitine; PM: plasma membrane; SD-N: synthetic defined medium without amino acids and ammonium sulfate; TOR: target of rapamycin; VASt: VAD1 Analog of StAR-related lipid transfer; YFP, yellow fluorescent protein.
DOI: 10.6084/m9.figshare.7460096.v1
title: Additional file 9: of Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture

description: Table S5. The original RNA-seq data for GhGH3 expression pattern analysis. (XLSX 20â kb)
DOI: 10.6084/m9.figshare.7460126
title: Additional file 3: of Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing

description: Figure S3. Heat map of the genetic linkage map. (ZIP 3270 kb)
DOI: 10.6084/m9.figshare.14275803.v1
title: Fluorofenidone inhibits epithelial-mesenchymal transition in human lens epithelial cell line FHL 124: a promising therapeutic strategy against posterior capsular opacification

description: ABSTRACT Purpose: The present study aimed to investigate the inhibitory effect of fluorofenidone against transforming growth factor β2-induced proliferation and epithelial-mesenchymal transition in human lens epithelial cell line FHL 124 and its potential mechanism. Methods: We evaluated the effect of fluorofenidone on proliferation and epithelial-mesenchymal transition of human lens epithelial cell line FHL 124 in vitro. After treatment with 0, 0.1, 0.2, 0.4, 0.6, and 1.0 mg/mL fluorofenidone, cell proliferation was measured via MTT assay. Cell viability was evaluated by lactate dehydrogenase activity from damaged cells. FHL 124 cells were treated with different transforming growth factor β2 concentrations (0-10 ng/mL) for 24 h and the expression of CTGF, α-SMA, COL-I, E-cadherin, and Fn were detected via quantitative polymerase chain reaction and Western blot analysis. After treatment with 0, 0.2, and 0.4 mg/ml fluorofenidone, the expressions of transforming growth factor β2 and SMADs were detected with real-time polymerase chain reaction and Western blot analysis. Expressions of CTGF, α-SMA, COL-I, and Fn were analyzed by immunocytochemistry assay. Results: The viability of FHL 124 cells was not inhibited when the fluorofenidone concentration was ≤0.4 mg/mL after the 24h treatment. Cytotoxicity was not detected via lactate dehydrogenase assay after the 24h and 36h treatment with 0.2 and 0.4 mg/mL fluorofenidone. Transforming growth factor β2 increased mRNA and protein expression of CTGF, α-SMA, COL-I, and Fn. However, fluorofenidone significantly suppressed expression of SMADs, CTGF, α-SMA, COL-I, and Fn in the absence or presence of transforming growth factor β2 stimulation. Conclusions: Fluorofenidone significantly inhibited expression of SMADs, CTGF, α-SMA, COL-I, and Fn in FHL 124 cells. Due to noncompliance in infants, fluorofenidone may become a novel therapeutic drug against posterior capsular opacification in infants.
DOI: 10.6084/m9.figshare.7460207.v1
title: Additional file 1: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: One hundred twelve core germplasms used for SNP genotyping. (XLSX 14â kb)
DOI: 10.6084/m9.figshare.13227312
title: A VASt-domain protein regulates autophagy, membrane tension, and sterol homeostasis in rice blast fungus

description: Sterols are a class of lipids critical for fundamental biological processes and membrane dynamics. These molecules are synthesized in the endoplasmic reticulum (ER) and are transported bi-directionally between the ER and plasma membrane (PM). However, the trafficking mechanism of sterols and their relationship with macroautophagy/autophagy are still poorly understood in the rice blast fungus <i>Magnaporthe oryzae</i>. Here, we identified the VAD1 Analog of StAR-related lipid transfer (VASt) domain-containing protein MoVast1 via co-immunoprecipitation in <i>M. oryzae</i>. Loss of <i>MoVAST1</i> resulted in conidial defects, impaired appressorium development, and reduced pathogenicity. The MoTor (target of rapamycin in <i>M. oryzae</i>) activity is inhibited because MoVast1 deletion leads to high levels of sterol accumulation in the PM. Site-directed mutagenesis showed that the 902 T site is essential for localization and function of MoVast1. Through filipin or Flipper-TR staining, autophagic flux detection, MoAtg8 lipidation, and drug sensitivity assays, we uncovered that MoVast1 acts as a novel autophagy inhibition factor that monitors tension in the PM by regulating the sterol content, which in turn modulates the activity of MoTor. Lipidomics and transcriptomics analyses further confirmed that MoVast1 is an important regulator of lipid metabolism and the autophagy pathway. Our results revealed and characterized a novel sterol transfer protein important for <i>M. oryzae</i> pathogenicity. <b>Abbreviations:</b> AmB: amphotericin B; ATMT: <i>Agrobacterium tumefaciens</i>-mediated transformation; CM: complete medium; dpi: days post-inoculation; ER: endoplasmic reticulum; Flipper-TR: fluorescent lipid tension reporter; GO: Gene ontology; hpi: hours post-inoculation; IH: invasive hyphae; KEGG: kyoto encyclopedia of genes and genomes; MoTor: target of rapamycin in <i>Magnaporthe oryzae</i>; PalmC: palmitoylcarnitine; PM: plasma membrane; SD-N: synthetic defined medium without amino acids and ammonium sulfate; TOR: target of rapamycin; VASt: VAD1 Analog of StAR-related lipid transfer; YFP, yellow fluorescent protein.
DOI: 10.24403/jp.1330389
title: Braune, W., Leman, A. & Taubert, H.: Pflanzenanatomisches Praktikum : I. Zur Einführung in die Anatomie der Vegetationsorgane der Samenpflanzen. - 7. Aufl. - Jena ; Stuttgart : Gustav Fischer Verlag, 1994 / [rezensiert von] H. Manitz
DOI: 10.6084/m9.figshare.7460213
title: Additional file 2: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: qPCR primer sequences of favorable SNPs and reference gene. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460237
title: Additional file 5: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: SNPs generated from GLM and MLM analysis when Pâ &lt;â 0.01. (XLSX 364â kb)
DOI: 10.6084/m9.figshare.12703112
title: Data supporting an immune checkpoint score system for prognostic evaluation and adjuvant chemotherapy selection in patients with gastric cancer

description: This dataset consists of 5 files: 3 raw data files in <b>.xlsx</b> spreadsheet format and 2 code files in <b>.txt </b>format. These data and code files support the claims of the related manuscript: "A Promising Immune Checkpoint System in Gastric Cancer: Better Prognostic Evaluation and Effective Adjuvant Chemotherapy Selection".<br>The files are as follows:- Raw data of internal modelling set20200724.xlsx<br>- Raw data of Tissue microarray20200724.xlsx<br>- Raw date of external validation set20200724.xlsx- Annex 2 C-index corresponding code.txt- Annex 3 AIC corresponding code.txt<br>An additional code file entitled "Annex 1 Lasso corresponding code.txt" was used, but is not publicly available due to copyright restrictions.<br>The related study established a comprehensive immune scoring system based on 6 immunosuppressive ligands (NECTIN2, CEACAM1, HMGB1, SIGLEC6, CD44, and CD155) using the LASSO method to improve prognostic accuracy and provide an additional selection strategy for adjuvant chemotherapy of gastric cancer.