cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19518477
title: Additional file 2 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 2: Table S2. Lineage assignment for 142 high quality patient samples from UCLA health.
DOI: 10.6084/m9.figshare.13227312.v2
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.19518486.v1
title: Additional file 5 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 5: Table S5. Parameters for effective reproductive number estimation.
DOI: 10.6084/m9.figshare.19518587
title: Additional file 3 of TMT-based proteomic analysis reveals integrins involved in the synergistic infection of reticuloendotheliosis virus and avian leukosis virus subgroup J

description: Additional file 3: Table S1. The significant differentially expressed proteins were quantified by analyzing the MS/MS spectra.
DOI: 10.6084/m9.figshare.19518587.v1
title: Additional file 3 of TMT-based proteomic analysis reveals integrins involved in the synergistic infection of reticuloendotheliosis virus and avian leukosis virus subgroup J

description: Additional file 3: Table S1. The significant differentially expressed proteins were quantified by analyzing the MS/MS spectra.
DOI: 10.6084/m9.figshare.7460213.v1
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.7460246
title: Additional file 6: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: Common significant SNPs in GLM analysis and MLM analysis. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.14275731
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.19518593.v1
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.7460258.v1
title: Additional file 8: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: Additional SNP loci near the Marker20170â 64. (XLSX 10â kb)
DOI: 10.6084/m9.figshare.19518486
title: Additional file 5 of Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

description: Additional file 5: Table S5. Parameters for effective reproductive number estimation.
DOI: 10.6084/m9.figshare.7460126.v1
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.7460132
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.19518954
title: Phenotypic and transcriptomic characterization of an ABA-sensitive mutant generated by microspore embryogenesis in barley

description: Barley (<i>Hordeum vulgare</i> L.) has been recognized as an ideal model plant to study the mechanism of environmental adaptation for crop improvement owing to its wide adaption to abiotic stresses. Abscisic acid is an essential hormone involved in many abiotic stresses. Here, an ABA-sensitive barley mutant (<i>abas1</i>) was generated by microspore embryogenesis. On exogenous ABA treatment, the seedlings of <i>abas1</i> presented less plant height, root length, shoot and root dry matter than the wild type, and more genes showedigher expressional intensity and up-regulation models by RNA-Seq profiling. The gene ontology analysis revealed that the regulation of DEGs may lead to the activation of the ROS pathway and consumption of more energy in <i>abas1,</i> specifically. Furthermore, the up-regulation of two candidate genes (<i>P450</i> and <i>NsLTP</i>) in <i>abas1</i> may contribute to the variation of ABA sensitivity. Our findings provide more valuable material and information toward the understanding of the mechanism of ABA response in barley.
DOI: 10.6084/m9.figshare.20043166.v1
title: Analysis of virginiamycin M1 in swine feed, muscle and liver samples by quantum dots-based fluorescent immunochromatographic assay

description: Based on a highly sensitive and specific monoclonal antibody (mAb) against virginiamycin M1 (VIR M1), a quantum dots-based fluorescent immunochromatographic assay (QDs-ICA) for quick and sensitive analysis of VIR M1 was established for the first time. The mAb showed a half-maximal inhibitory concentration (IC<sub>50</sub>) of 0.5 ng/mL and cross-reactivity (CR) values below 0.1% for other three analogues when used in enzyme-linked immunosorbent assay (ELISA). The mAb was conjugated to ZnCdSe/ZnS (core/shell) QDs with maximum emission wavelength of 610 nm (orange-red) which was selected as fluorescent probe to increase QDs-ICA sensitivity. The cut-off value of QDs-ICA was 12.5 ng/mL. QDs-ICA showed a linear range from 0.7 to 14.5 ng/mL with a limit of quantification of 0.7 ng/mL. Compared with existing methods for the analysis of VIR M1, the QDs-ICA exhibited higher sensitivity. For analysis of VIR M1 concentrations spiked into swine feed, muscle and liver samples, recovery rates ranged from 94.0% to 111.6% with the highest coefficient of variation (CV) of 6.7% for intra-assay, and for inter-assay ranged from 94.7% to 107.6% with the highest CV of 9.4%. In conclusion, the QDs-ICA could be a potential method for analyzing VIR M1 in animal feed and animal-derived food.
DOI: 10.6084/m9.figshare.19518962
title: Transcriptomic insights into the regulatory networks of chilling-induced early flower in tobacco (<i>Nicotiana tabacum</i> L.)

description: Appropriate timing of flowering is pivotal for tobacco, while chilling stress occurring at the seedling stage often undesirably leads to early flowering. However, the potential mechanism underlying chilling-induced early flowering remains unknown. Here, transcriptome sequencing was performed in tobacco with or without chilling at both seedling and budding stages. Chilling affected the expression of numerous genes at the seedling stage, while these dramatic expression changes were largely eliminated at the budding stage. A small number of genes related to metabolism, flower development, and stress tolerance continued to keep their altered expression patterns from the seedling stage to the budding stage. Many potential flowering-related genes involved in flowering pathways were identified and over half of them were differentially expressed. Functional analysis revealed that the down-regulation of <i>NbXTH22</i> rendered tobacco less sensitive to chilling-induced early flowering. These results provide valuable resources for the investigation of flowering regulatory mechanisms and contribute to the genetic improvement of crops.
DOI: 10.6084/m9.figshare.20043166
title: Analysis of virginiamycin M1 in swine feed, muscle and liver samples by quantum dots-based fluorescent immunochromatographic assay

description: Based on a highly sensitive and specific monoclonal antibody (mAb) against virginiamycin M1 (VIR M1), a quantum dots-based fluorescent immunochromatographic assay (QDs-ICA) for quick and sensitive analysis of VIR M1 was established for the first time. The mAb showed a half-maximal inhibitory concentration (IC<sub>50</sub>) of 0.5 ng/mL and cross-reactivity (CR) values below 0.1% for other three analogues when used in enzyme-linked immunosorbent assay (ELISA). The mAb was conjugated to ZnCdSe/ZnS (core/shell) QDs with maximum emission wavelength of 610 nm (orange-red) which was selected as fluorescent probe to increase QDs-ICA sensitivity. The cut-off value of QDs-ICA was 12.5 ng/mL. QDs-ICA showed a linear range from 0.7 to 14.5 ng/mL with a limit of quantification of 0.7 ng/mL. Compared with existing methods for the analysis of VIR M1, the QDs-ICA exhibited higher sensitivity. For analysis of VIR M1 concentrations spiked into swine feed, muscle and liver samples, recovery rates ranged from 94.0% to 111.6% with the highest coefficient of variation (CV) of 6.7% for intra-assay, and for inter-assay ranged from 94.7% to 107.6% with the highest CV of 9.4%. In conclusion, the QDs-ICA could be a potential method for analyzing VIR M1 in animal feed and animal-derived food.
DOI: 10.6084/m9.figshare.7460414
title: Additional file 4: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S3. Expression of genes that were known as dehydration inducible genes (ELIP, GS, beta-amylase, catalase, LEA etc.). (XLSX 22â kb)
DOI: 10.6084/m9.figshare.7460207
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.7460222
title: Additional file 3: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: Primers and functional description of candidate genes. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.12703112.v1
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.
DOI: 10.6084/m9.figshare.14276132.v1
title: Morphological and physiological properties of hybrid rice seeds with top-gray chalkiness

description: ABSTRACT Hybrid rice seeds from sterile lines have displayed a new type of heavy chalkiness in the subtropical zone of China in recent years, which was named top-gray chalkiness, resulting in a lower quality of hybrid rice seeds in large-scale production. In this study, the morphological characteristics of the chalky hybrid rice seeds were investigated, the microscopic structures of their chalky parts observed, the α-amylase activit and relative nutrient content analyzed, and the germination indexe and microorganism populations of the chalky hybrid seeds determined. The results revealed that top-gray chalkiness in hybrid rice seeds originated from the top site of the grain, and that the chalky part was probably infected by bacteri and fungi to form a gray colo and which further resulted in a lower germination rat and germination potential. This observed chalkiness in rice seeds differed from the previously reported rice chalkiness categories both in the occurrence positio and color. Besides, the amylopectin content declined in the chalky par and the protein content in the chalky part increased as compared to the normal seeds. This research could provide technical support for the hybrid rice breeding enterprises during the breeding of hybrid rice seeds in large-scale production.
DOI: 10.6084/m9.figshare.7460246.v1
title: Additional file 6: of Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

description: Common significant SNPs in GLM analysis and MLM analysis. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460396.v1
title: Additional file 1: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S1. Summary of transcriptomic data of de novo assembly of fresh, dehydrated and rehydrated Haberlea rhodopensis. (XLSX 10â kb)
DOI: 10.6084/m9.figshare.7460408
title: Additional file 3: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S2. Reads and base numbers of raw and clean sequences from ten libraries. (XLSX 10â kb)
DOI: 10.6084/m9.figshare.7460435
title: Additional file 6: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S4. Designed primers for the qPCR experiment in this article. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460435.v1
title: Additional file 6: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S4. Designed primers for the qPCR experiment in this article. (XLSX 11â kb)
DOI: 10.6084/m9.figshare.7460441
title: Additional file 7: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S5. GO enrichment of up- and down-regulated unigenes of each stage. (XLSX 13â kb)
DOI: 10.6084/m9.figshare.7460498
title: Additional file 2: of Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis

description: Table S1. Details of significant SNPs related to SS2 susceptibility. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.7460507
title: Additional file 2: of A spatiotemporal meta-analysis of HIV/syphilis epidemic among men who have sex with men living in mainland China

description: Dataset listing extracted data of 272 articles included. The dataset includes periodic and demographic information, the crude HIV and syphilis prevalence rate, and history of condom use with male partner, female, and unprotected sex with casual male partner. (XLSX 37 kb)
DOI: 10.6084/m9.figshare.7460528
title: Additional file 6: of Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis

description: Table S5. Details of GO classification. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7460528.v1
title: Additional file 6: of Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis

description: Table S5. Details of GO classification. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.7460531
title: Additional file 7: of Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis

description: Table S6. Details of GO over-representation. (XLSX 12 kb)
DOI: 10.6084/m9.figshare.23706901.v1
title: Additional file 2 of Causal association between body mass index and temporomandibular disorders: a bidirectional two-sample Mendelian randomization analysis

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.23706904
title: Additional file 3 of Causal association between body mass index and temporomandibular disorders: a bidirectional two-sample Mendelian randomization analysis

description: Supplementary Material 3
DOI: 10.6084/m9.figshare.7460450
title: Additional file 8: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S6. Pathways identified from the functionally organized GO/pathway term network using DEGs in D20 stage. (XLSX 13â kb)
DOI: 10.6084/m9.figshare.23706907.v1
title: Additional file 4 of Causal association between body mass index and temporomandibular disorders: a bidirectional two-sample Mendelian randomization analysis

description: Supplementary Material 4
DOI: 10.6084/m9.figshare.7460537.v1
title: Additional file 8: of Screening of Streptococcus Suis serotype 2 resistance genes with GWAS and transcriptomic microarray analysis

description: Table S7. SNPs significant to SS2 susceptibility and corresponding DEGs located within their 500â kb high correlation range. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7460408.v1
title: Additional file 3: of Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis

description: Table S2. Reads and base numbers of raw and clean sequences from ten libraries. (XLSX 10â kb)
DOI: 10.6084/m9.figshare.14276106.v1
title: Improving seed germination and seedling growth of guava under heat and osmotic stresses by chemical and hormonal seed treatments

description: ABSTRACT This study, consisting of two independent experiments, was conducted to optimize presowing guava seed treatments and evaluate the optimized treatments in improving germination and seedling growth of guava under heat and osmotic stresses. In the first experiment, seeds of guava cultivar White Flesh Local I were soaked in water, gibberellic acid (GA3) (0.05 and 0.1%), hydrochloric acid (HCl) (5 and 10%) and sulfuric acid (H2SO4) (5 and 10%) for 24 and 48 h (for water and GA3), and 2 and 5 min (for HCl and H2SO4). Seed soaking (priming) with GA3 (0.1%, at 48 h) and HCl (10%, 2 min) were the most effective treatments to improve seed germination and early seed growth of guava and were used in the second experiment. In the second experiment, treated and untreated seeds were sown in plastic boxes between two layers of filter papers maintained at osmotic potentials of 0, -1.5 and -3 MPa. The germination boxes were incubated at optimal (25 °C) and higher (32 °C) temperatures. Germination was significantly suppressed at a higher temperature and with an increase in the osmotic potential. However, seed treatments with GA3 and HCl were effective to improve the germination and seedling growth of guava under both temperature and osmotic stresses. In conclusion, chemical and hormonal seed treatments may help improve the seed germination and seedling growth of guava under heat and osmotic stresses by modulation of antioxidant enzymes and leaf proline. Seed treatment with GA3 (0.1%, 48 h) was the most effective in this regard.