cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12853362
title: <i>In silico</i> designing of multi-epitope vaccine construct against human coronavirus infections

description: Single stranded RNA viruses were known to cause variety of diseases since many years and are gaining much importance due to pandemic after the identification of a novel corona virus (severe acute respiratory syndrome-coronavirus (SARS-CoV-2)). Seven coronaviruses (CoVs) are known to infect humans and they are OC43 CoV, NL63 CoV, HKU1 CoV, Middle East respiratory syndrome, SARS CoV, and SARS CoV-2. Virus replication weakens the immune system of host thereby altering T-cell count and much of interferon response. Although no vaccine or therapeutic treatment has been approved till now for CoV infection, trials of vaccine against SARS CoV-2 are in progress. One of the epitopes used for vaccine production is of the spike protein on the surface of virus. The work focuses on designing of multi-epitope vaccine construct for treatment of seven human CoV infections using the epitopes present on the spike protein of human CoVs. To address this, immuno-informatics techniques have been employed to design multi-epitope vaccine construct. B- and T-cell epitopes of the spike proteins have been predicted and designed into a multi-epitope vaccine construct. The tertiary structure of the vaccine construct along with the adjuvant has been modelled and the physiochemical properties have been predicted. The multi-epitope vaccine construct has antigenic and non-allergenic property. After validation, refinement and disulphide engineering of the vaccine construct, molecular docking with toll-like receptors (TLRs) have been performed. Molecular dynamics simulation in aqueous environment predicted that the vaccine-TLRs complexes were stable. The vaccine construct is predicted to be able to trigger primary immune response <i>in silico</i>. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8057903
title: Additional file 6: of High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

description: Table S6. Phenotypic data of FFN of RILs and parents in three seasons. (XLSX 16 kb)
DOI: 10.6084/m9.figshare.16970744.v2
title: Network pharmacology and experimental validation to explore the molecular mechanisms of Bushen Huoxue for the treatment of premature ovarian insufficiency

description: Bushen Huoxue (BSHX) has been applied in clinical traditional Chinese medicine treatment, and has definitive clinical efficacy in the treatment of Premature Ovarian Insufficiency (POI) in China. However, little is known of the underlying mechanism of BSHX. The purpose of this paper is to study the pharmacological mechanisms of BSHX acting on POI based on a pharmacology and experimental validation. The pharmacological database of chinese medicine system and analysis platform (TCMSP) were used to search the effective active ingredients and potential action targets of BSHX. Drugbank, Online Mendelian Inheritance in Man (OMIM), Genecards, and Disgenet databases were used to obtain relevant targets of POI. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and the visual network of protein-protein interaction network were constructed by FunRich3.1. Pymol software, and Auto Dock tools 1.5.6 were used for molecular docking. Murine model of POI was used to further investigate the mechanism of BSHX against on POI. Finally, 127 active compounds were collected from TCMSP database, and 215 active targets were identified. There were 1366 targets related to POI and 99 targets of BSHX for the treatment of POI. Quercetin, kaempferol, and stigmasterol were recognized as the most effective compounds corresponding to targets. The top three genes according to degree value are TP53, Akt1, and VEGFA. Further, the results of GO and KEGG enrichment analysis revealed that those core targets were mainly enriched on TRAIL and TGF-β receptor signaling. The results of molecular docking showed that stigmasterol had good binding ability to Akt1. Moreover, experimental validation suggests that BSHX significantly Increased the expression of TGF-β1 and Smad2/3, regulating the release of serum sex hormones, which include Follicular stimulating hormone (FSH), Estradiol (E2), and Antimullerin hormone (AMH). BSHX treats POI by regulating TGF-β1 and Smad2/3 signaling pathways; Quercetin, kaempferol, and stigmasterol were the most effective compounds in BSHX.
DOI: 10.6084/m9.figshare.16970741.v1
title: MicroRNA-223-3p is involved in fracture healing by regulating fibroblast growth factor receptor 2

description: MicroRNAs (miRNAs) are powerful modulators of fracture healing. The research explored the level of serum miR-223-3p in fracture patients and its potential mechanism in fracture healing. In the study, miR-223-3p levels in 42 patients with intra-articular fracture and 40 patients with hand fracture were detected by real-time fluorescence quantitative PCR reaction (qRT-PCR). Subsequently, osteoblasts MC3T3-E1 was transfected with miR-223-3p mimic or inhibitor, and cell function was detected by Cell counting kit (CCK-8) assay and flow cytometry. Dual-luciferase reporter assay verified the regulation mechanism of miR-223-3p and its target genes. We found that miR-223-3p was significantly elevated over time in patients with intra-articular fracture and hand fracture compared with healthy individuals. Moreover, increased miR-223-3p significantly reduced cell viability and promoted cell apoptosis. The fibroblast growth factor receptor 2 (FGFR2) was the target of miR-223-3p. Serum FGFR2 was significantly decreased in patients, which was contrary to the expression of miR-223-3p. Moreover, FGFR2 levels in cells were negatively regulated by miR-223-3p. Finally, si-FGFR2 significantly reversed the promotion of miR-223-3p inhibitor on cell viability and the inhibition of cell apoptosis. Our research suggested that miR-223-3p is highly expressed in fracture patients, and regulates osteoblast cell viability and apoptosis by targeting FGFR2. This may be a valuable target for fracture healing therapy and provide a new perspective for its treatment.
DOI: 10.6084/m9.figshare.21688994
title: A Random Projection Approach to Hypothesis Tests in High-Dimensional Single-Index Models

description: In this article, we consider the problem of hypothesis testing in high-dimensional single-index models. First, we study the feasibility of applying the classical F-test to a single-index model when the dimension of covariate vector and sample size are of the same order, and derive its asymptotic null distribution and asymptotic local power function. For the ultrahigh-dimensional single-index model, we construct F-statistics based on lower-dimensional random projections of the data, and establish the asymptotic null distribution and the asymptotic local power function of the proposed test statistics for the hypothesis testing of global and partial parameters. The new proposed test possesses the advantages of having a simple structure as well as being easy to compute. We compare the proposed test with other high-dimensional tests and provide sufficient conditions under which the proposed tests are more efficient. We conduct simulation studies to evaluate the finite-sample performances of the proposed tests and demonstrate that it has higher power than some existing methods in the models we consider. The application of real high-dimensional gene expression data is also provided to illustrate the effectiveness of the method. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8057921
title: Additional file 8: of High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

description: Table S8. Summary of differential expression genes just before and after the first flower emerging. (XLSX 1683 kb)
DOI: 10.6084/m9.figshare.21689045
title: A Covariate-Regulated Sparse Subspace Learning Model and Its Application to Process Monitoring and Fault Isolation

description: Multivariate functional data are increasingly common in various applications. The cross-correlation of different process variables is typically complex in that a variable might be weakly correlated or not correlated with most of the other variables, and the cross-correlation is time-varying and might be regulated by some exogenous covariates. To address these two challenges, we propose a covariate-regulated sparse subspace learning (CSSL) model. We consider the scenario that these process variables lie in multiple subspaces, and only process variables from the same subspace are cross-correlated with each other. To take into account the effect of the exogenous covariates on the subspace structure, we partition the domain of the covariates into a number of regions. In each region, the subspace structure is treated as constant and can be learned independently. An efficient decision-tree-based algorithm is then proposed to obtain the solution. The proposed method can be further applied to process monitoring and fault isolation for multivariate processes. The efficacy of this method is demonstrated by comprehensive simulations and a case study on a dataset from the supervisory control and data acquisition (SCADA) system of the wind turbine.
DOI: 10.6084/m9.figshare.21689045.v1
title: A Covariate-regulated Sparse Subspace Learning Model and Its Application to Process Monitoring and Fault Isolation

description: Multivariate functional data are increasingly common in various applications. The cross-correlation of different process variables is typically complex in that a variable might be weakly correlated or not correlated with most of the other variables, and the cross-correlation is time-varying and might be regulated by some exogenous covariates. To address these two challenges, we propose a covariate-regulated sparse subspace learning (CSSL) model. We consider the scenario that these process variables lie in multiple subspaces, and only process variables from the same subspace are cross-correlated with each other. To take into account the effect of the exogenous covariates on the subspace structure, we partition the domain of the covariates into a number of regions. In each region, the subspace structure is treated as constant and can be learned independently. An efficient decision-tree-based algorithm is then proposed to obtain the solution. The proposed method can be further applied to process monitoring and fault isolation for multivariate processes. The efficacy of this method is demonstrated by comprehensive simulations and a case study on a dataset from the supervisory control and data acquisition (SCADA) system of the wind turbine. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.21689045.v2
title: A Covariate-Regulated Sparse Subspace Learning Model and Its Application to Process Monitoring and Fault Isolation

description: Multivariate functional data are increasingly common in various applications. The cross-correlation of different process variables is typically complex in that a variable might be weakly correlated or not correlated with most of the other variables, and the cross-correlation is time-varying and might be regulated by some exogenous covariates. To address these two challenges, we propose a covariate-regulated sparse subspace learning (CSSL) model. We consider the scenario that these process variables lie in multiple subspaces, and only process variables from the same subspace are cross-correlated with each other. To take into account the effect of the exogenous covariates on the subspace structure, we partition the domain of the covariates into a number of regions. In each region, the subspace structure is treated as constant and can be learned independently. An efficient decision-tree-based algorithm is then proposed to obtain the solution. The proposed method can be further applied to process monitoring and fault isolation for multivariate processes. The efficacy of this method is demonstrated by comprehensive simulations and a case study on a dataset from the supervisory control and data acquisition (SCADA) system of the wind turbine.
DOI: 10.6084/m9.figshare.8057879.v1
title: Additional file 2: of High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

description: Table S2. List of marker names, linkage groups, and genetic distances of 9328 SLAF markers in the genetic map of pepper. (XLS 1118 kb)
DOI: 10.6084/m9.figshare.19582254
title: Additional file 10 of Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.)

description: Additional file10: Table S9. The primers used for qRT-PCR in this study.
DOI: 10.6084/m9.figshare.8057915
title: Additional file 7: of High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

description: Table S7. List of 59 candidate genes located in the major QTLs Ffn2.1 and Ffn2.2. (XLSX 21 kb)
DOI: 10.6084/m9.figshare.19582255.v1
title: Additional file 2 of Distributions and trends of the global burden of COPD attributable to risk factors by SDI, age, and sex from 1990 to 2019: a systematic analysis of GBD 2019 data

description: Additional file 2: Figure S1. Age-standardized rate of SEV of 8 main risk factors by SDI quintiles and sex from 1990 to 2019. Figure S2. Contributions of 8 main risk factors to the PAF of age-standardized death due to chronic obstructive pulmonary disease by different SDI quintiles and sexes from 1990 to 2019. Figure S3. Contributions of 8 main risk factors to the PAF of age-standardized YLD due to chronic obstructive pulmonary disease by different SDI quintiles and sexes from 1990 to 2019. Figure S4. Contributions of 8 main risk factors to the PAF of age-standardized YLL due to chronic obstructive pulmonary disease by different SDI quintiles and sexes from 1990 to 2019. Figure S5. The global burden of COPD attributable to occupational particles over the past 30 years. Figure S6. The global burden of COPD attributable to secondhand smoke over the past 30 years. Figure S7. The global burden of COPD attributable to ambient ozone pollution over the past 30 years. Figure S8. The global burden of COPD attributable to high temperature over the past 30 years. Figure S9. The global burden of COPD attributable to low temperature over the past 30 years.
DOI: 10.6084/m9.figshare.8057999
title: Additional file 11: of Genetic architecture of grain yield in bread wheat based on genome-wide association studies

description: Table S7. Phenotypic data in each environment and BLUE value for grain yield and related traits in the diverse panel. GY, grain yield; SN, spike number per square meter; KNS, kernel number per spike; TKW, thousand-kernel weight; KL, kernel length; KW, kernel width; SL, spike length; SDW, spike dry weight; HD, heading date; PH, plant height; UIL, uppermost internode length; FLL, flag leaf length; FLW, flag leaf width. (XLSX 151 kb)
DOI: 10.6084/m9.figshare.16970744.v1
title: Network Pharmacology and Experimental Validation to Explore the Molecular Mechanisms of Bushen Huoxue for the Treatment of Premature Ovarian Insufficiency

description: Bushen Huoxue (BSHX) has been applied in clinical traditional Chinese medicine treatment, and has definitive clinical efficacy in the treatment of Premature Ovarian Insufficiency (POI) in China. However, little is known of the underlying mechanism of BSHX. The purpose of this paper is to study the pharmacological mechanisms of BSHX acting on POI based on a pharmacology and experimental validation. The pharmacological database of chinese medicine system and analysis platform (TCMSP) were used to search the effective active ingredients and potential action targets of BSHX. Drugbank, Online Mendelian Inheritance in Man (OMIM), Genecards, and Disgenet databases were used to obtain relevant targets of POI. Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and the visual network of protein-protein interaction network were constructed by FunRich3.1. Pymol software, and Auto Dock tools 1.5.6 were used for molecular docking. Murine model of POI was used to further investigate the mechanism of BSHX against on POI. Finally, 127 active compounds were collected from TCMSP database, and 215 active targets were identified. There were 1366 targets related to POI and 99 targets of BSHX for the treatment of POI. Quercetin, kaempferol, and stigmasterol were recognized as the most effective compounds corresponding to targets. The top three genes according to degree value are TP53, Akt1, and VEGFA. Further, the results of GO and KEGG enrichment analysis revealed that those core targets were mainly enriched on TRAIL and TGF-β receptor signaling. The results of molecular docking showed that stigmasterol had good binding ability to Akt1. Moreover, experimental validation suggests that BSHX significantly Increased the expression of TGF-β1 and Smad2/3, regulating the release of serum sex hormones, which include Follicular stimulating hormone (FSH), Estradiol (E2), and Antimullerin hormone (AMH).
DOI: 10.6084/m9.figshare.16970740.v1
title: Insulin-like growth factor 2 mRNA binding protein 2 regulates proliferation, migration and angiogenesis of keratinocytes by modulating heparanase stability

description: Wound healing is related to proliferation, migration and angiogenesis of keratinocytes. Insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) is an important N6-methyladenosine (m6A) reader, which is involved in multiple processes, including wound healing. However, the function and mechanism of IGF2BP2 in keratinocyte processes are largely uncertain. In the present study, expression levels of IGF2BP2 and heparanase (HPSE) were detected by quantitative reverse transcription polymerase chain reaction and western blotting assays. Cell proliferation was investigated with cell counting kit-8 analysis. Cell migration was determined through wound healing assay. Angiogenesis was measured by tube formation assay and vascular endothelial growth factor (VEGF) level using enzyme linked immunosorbent assay. The interaction between IGF2BP2 and HPSE was analyzed by RNA immunoprecipitation, pull-down and luciferase reporter analyses. The results showed that IGF2BP2 expression was enhanced in wound healing. IGF2BP2 downregulation constrained HaCaT cell proliferation, migration and angiogenesis. IGF2BP2 knockdown decreased HPSE expression. IGF2BP2 could regulate HPSE stability by binding with 3ʹ untranslated region (UTR) of HPSE. HPSE upregulation attenuated silencing IGF2BP2-mediated suppression of proliferation, migration and angiogenesis. As a conclusion, IGF2BP2 knockdown repressed proliferation, migration and angiogenesis of HaCaT cells by decreasing HPSE stability.
DOI: 10.6084/m9.figshare.8057879
title: Additional file 2: of High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.)

description: Table S2. List of marker names, linkage groups, and genetic distances of 9328 SLAF markers in the genetic map of pepper. (XLS 1118 kb)
DOI: 10.6084/m9.figshare.19582260.v1
title: Additional file 2 of Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.)

description: Additional file2: Table S1. The detailed information of 113 TaVQ genes identified in wheat genome.
DOI: 10.6084/m9.figshare.19582254.v1
title: Additional file 10 of Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.)

description: Additional file10: Table S9. The primers used for qRT-PCR in this study.
DOI: 10.6084/m9.figshare.13290952
title: Additional file 1 of A novel nomogram for predicting liver metastasis in patients with gastrointestinal stromal tumor: a SEER-based study

description: Additional file 1: Table S1. A database of the information of GIST patients obtained from SEER database.
DOI: 10.6084/m9.figshare.13290952.v1
title: Additional file 1 of A novel nomogram for predicting liver metastasis in patients with gastrointestinal stromal tumor: a SEER-based study

description: Additional file 1: Table S1. A database of the information of GIST patients obtained from SEER database.
DOI: 10.6084/m9.figshare.8058002
title: Additional file 12: of Genetic architecture of grain yield in bread wheat based on genome-wide association studies

description: Table S8. Genotypic data for the diverse panel of 166 elite wheat varieties. (XLSX 218034 kb)
DOI: 10.6084/m9.figshare.8058002.v1
title: Additional file 12: of Genetic architecture of grain yield in bread wheat based on genome-wide association studies

description: Table S8. Genotypic data for the diverse panel of 166 elite wheat varieties. (XLSX 218034 kb)
DOI: 10.6084/m9.figshare.19582320.v1
title: Additional file 3 of miRNA sequencing analysis of healthy and atretic follicles of chickens revealed that miR-30a-5p inhibits granulosa cell death via targeting Beclin1

description: Additional file 3: Table S1. Summary of data generated from small RNA deep sequencing.
DOI: 10.6084/m9.figshare.19582329.v1
title: Additional file 6 of miRNA sequencing analysis of healthy and atretic follicles of chickens revealed that miR-30a-5p inhibits granulosa cell death via targeting Beclin1

description: Additional file 6: Table S4. miR-148a-3p predict target genes.
DOI: 10.6084/m9.figshare.13290955
title: Additional file 2 of A novel nomogram for predicting liver metastasis in patients with gastrointestinal stromal tumor: a SEER-based study

description: Additional file 2: Table S2. A database of training set.
DOI: 10.5281/zenodo.10653474
title: Dataset for the article: "First Principles Study on the Structural and Magnetic Properties of Low-Index Cu2O and CuO Surfaces"

description: This data set contains the main input and output files of the calculations performed for the article: "First Principles Study on the Structural and Magnetic Properties of Low-Index Cu2O and CuO Surfaces"
DOI: 10.5281/zenodo.10653475
title: Dataset for the article: "First Principles Study on the Structural and Magnetic Properties of Low-Index Cu2O and CuO Surfaces"

description: This data set contains the main input and output files of the calculations performed for the article: "First Principles Study on the Structural and Magnetic Properties of Low-Index Cu2O and CuO Surfaces"
DOI: 10.6084/m9.figshare.19582332
title: Additional file 7 of miRNA sequencing analysis of healthy and atretic follicles of chickens revealed that miR-30a-5p inhibits granulosa cell death via targeting Beclin1

description: Additional file 7: Table S5. miR-30a-5p predict target genes.
DOI: 10.6084/m9.figshare.19582263
title: Additional file 3 of Genome-wide analysis of the VQ motif-containing gene family and expression profiles during phytohormones and abiotic stresses in wheat (Triticum aestivum L.)

description: Additional file3: Table S2. The VQ genes identified from Arabidopsis, rice, barley , and maize in this study.