cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12896667
title: A Set of Efficient Methods to Generate High-Dimensional Binary Data With Specified Correlation Structures

description: High-dimensional correlated binary data arise in many areas, such as observed genetic variations in biomedical research. Data simulation can help researchers evaluate efficiency and explore properties of different computational and statistical methods. Also, some statistical methods, such as Monte Carlo methods, rely on data simulation. Lunn and Davies proposed linear time complexity methods to generate correlated binary variables with three common correlation structures. However, it is infeasible to specify unequal probabilities in their methods. In this article, we introduce several computationally efficient algorithms that generate high-dimensional binary data with specified correlation structures and unequal probabilities. Our algorithms have linear time complexity with respect to the dimension for three commonly studied correlation structures, namely exchangeable, decaying-product and <i>K</i>-dependent correlation structures. In addition, we extend our algorithms to generate binary data of specified nonnegative correlation matrices satisfying the validity condition with quadratic time complexity. We provide an R package, CorBin, to implement our simulation methods. Compared to the existing packages for binary data generation, the time cost to generate a 100-dimensional binary vector with the common correlation structures and general correlation matrices can be reduced up to 10<sup>5</sup> folds and 10<sup>3</sup> folds, respectively, and the efficiency can be further improved with the increase of dimensions. The R package CorBin is available on CRAN at https://cran.r-project.org/.
DOI: 10.6084/m9.figshare.7252535.v1
title: Triglyceride glucose and haemoglobin glycation index for predicting outcomes in diabetes patients with new-onset, stable coronary artery disease: a nested case-control study

description: <b>Aim:</b> Previous studies have shown that both triglyceride glucose (TyG) and haemoglobin glycation indexes (HGI) are predictors of cardiovascular risk. However, the prognostic value of TyG index and HGI in patients with type 2 diabetes mellitus (T2DM) and stable coronary artery disease (CAD) is not determined. <b>Methods:</b> We conducted a nested case-control study among 1282 T2DM patients with stable CAD. Patients were followed up for 3846 person-years. A total of 160 patients with events (12.5%) were identified and matched individually on age, gender, previous use of lipid lowering agents and duration of follow-up with 640 controls. <b>Results:</b> In Kaplan–Meier analysis, the upper tertiles of TyG index and HGI had a significant lower event-free survival (<i>p</i> = .002; <i>p</i> = .036, respectively). Of the note, both TyG index and HGI were associated with increased risk of MACCEs after adjusting for confounding risk factors [adjusted HR (95% CI): 1.693 (1.238–2.316); 1.215 (1.046–1.411), respectively]. Moreover, adding TyG index to the Cox model increased the C-statistic to 0.638 (95%CI: 0.595–0.683, <i>p</i> = .002) while the C-statistic was not statistically improved when HGI was included (<i>p</i> = .240). <b>Conclusions:</b> Both TyG index and HGI could predict cardiovascular outcomes in T2DM patients with new-onset, stable CAD while TyG index might be better.Key messagesBoth TyG and HGI are predictors of cardiovascular risk.The prognostic value of TyG index and HGI in T2DM patients with stable coronary artery disease is not determined.Our study firstly indicates that TyG index might have better prognostic value than HGI in T2DM patients with new-onset, stable CAD. Both TyG and HGI are predictors of cardiovascular risk. The prognostic value of TyG index and HGI in T2DM patients with stable coronary artery disease is not determined. Our study firstly indicates that TyG index might have better prognostic value than HGI in T2DM patients with new-onset, stable CAD.
DOI: 10.6084/m9.figshare.13420718.v1
title: <i>Phlebopus roseus</i>, a new edible bolete from China, is associated with insects and plants

description: <i>Phlebopus roseus</i> is described as new based on collections from southwest China. Phylogenetic analyses of nuclear rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuclear 28S rDNA (28S), translation elongation factor 1-alpha (<i>tef1</i>), and the largest and second largest subunits of RNA polymerase II (<i>rpb1, rpb2</i>) support <i>P. roseus</i> as a novel species in the genus <i>Phlebopus</i> (Boletinellaceae, Boletales). The new species resembles <i>P. portentosus</i> but differs from it in that mature basidiomata have a bright rose-red-colored stipe and a radiate tubular hymenophore with nested pores. Despite extensive searching, <i>P. roseus</i> has only been found at four sites within a 24-hectare orchard dominated by <i>Eriobotrya japonica</i>, which is agriculturally important given its fruit production (loquats). Therefore, this species appears to be endemic and geographically restricted. The ecology of this bolete is also unique. In line with the trophic behavior of other species in the Boletinellaceae, our observations indicate that <i>P. roseus</i> forms a symbiotic association with the scale insect <i>Coccus hesperidum</i>, identified through sequence analysis of its mitochondrial cytochrome <i>c</i> oxidase subunit I (<i>COI</i>) region, to form fungus-insect galls that develop on roots of <i>E. japonica</i> trees. <i>Phlebopus roseus</i> is an edible mushroom species and is collected from the type location by farmers and sold commercially in limited quantities at local markets alongside <i>P. portentosus</i> and other fungi.
DOI: 10.6084/m9.figshare.19188240
title: MATLAB Codes from Multi-breather solutions to the Sasa–Satsuma equation

description: General breather solution to the Sasa–Satsuma equation (SSE) is systematically investigated in this paper. We firstly transform the SSE into a set of three Hirota bilinear equations under a proper plane wave boundary condition. Starting from a specially arranged tau-function of the Kadomtsev–Petviashvili hierarchy and a set of 11 bilinear equations satisfied, we implement a series steps of reduction procedure, i.e. C-type reduction, dimension reduction and complex conjugate reduction, and reduce these 11 equations to three bilinear equations for the SSE. Meanwhile, the general breather solution to the SSE is found in determinant of even order. The one- and two-breather solutions are calculated and analysed in detail.
DOI: 10.6084/m9.figshare.9751133
title: Additional file 1: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S1. The 50 most abundance OTUs in the glycine betaine (GBT)-amended microcosms and their relative abundance in the ‘heavy’, ‘light’ and unfractionated DNA during GBT enrichment. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9751133.v1
title: Additional file 1: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S1. The 50 most abundance OTUs in the glycine betaine (GBT)-amended microcosms and their relative abundance in the ‘heavy’, ‘light’ and unfractionated DNA during GBT enrichment. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9751139
title: Additional file 2: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S2. Summary of metagenome-assembled genomes (MAGs) from the GBT-stable isotope probing enrichment. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9751139.v1
title: Additional file 2: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S2. Summary of metagenome-assembled genomes (MAGs) from the GBT-stable isotope probing enrichment. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.9751145
title: Additional file 3: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S3. Metagenomes used for read-recruitment against Candidatus â Betaina sedimenttiâ . (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9751145.v1
title: Additional file 3: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S3. Metagenomes used for read-recruitment against Candidatus â Betaina sedimenttiâ . (XLSX 13 kb)
DOI: 10.6084/m9.figshare.9751151
title: Additional file 4: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S4. Samples subjected to amplicon sequencing of 16S rRNA genes in this study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9751151.v1
title: Additional file 4: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S4. Samples subjected to amplicon sequencing of 16S rRNA genes in this study. (XLSX 14 kb)
DOI: 10.6084/m9.figshare.9751160
title: Additional file 5: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S5. Annotation of MAG (Bin 4) by RAST (Rapid Annotation using Subsystem Technology). (XLS 3473 kb)
DOI: 10.6084/m9.figshare.9751160.v1
title: Additional file 5: of A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments

description: Table S5. Annotation of MAG (Bin 4) by RAST (Rapid Annotation using Subsystem Technology). (XLS 3473 kb)
DOI: 10.6084/m9.figshare.9751184
title: Additional file 1: of Sequential stimulation with different concentrations of BMP4 promotes the differentiation of human embryonic stem cells into dental epithelium with potential for tooth formation

description: Table S1. Presenting the primer used for qRT-PCR. (XLS 27 kb)
DOI: 10.6084/m9.figshare.9751184.v1
title: Additional file 1: of Sequential stimulation with different concentrations of BMP4 promotes the differentiation of human embryonic stem cells into dental epithelium with potential for tooth formation

description: Table S1. Presenting the primer used for qRT-PCR. (XLS 27 kb)
DOI: 10.6084/m9.figshare.9751187
title: MOESM1 of Genomic and phenotypic evaluation of rice susceptible check TN1 collected in Taiwan

description: Additional file 1: Table S1. SNPs across four rice accessions: Qingliu, TN1-NPGRC, TN1-TDARES, and TN1-NTU.
DOI: 10.6084/m9.figshare.9751187.v1
title: MOESM1 of Genomic and phenotypic evaluation of rice susceptible check TN1 collected in Taiwan

description: Additional file 1: Table S1. SNPs across four rice accessions: Qingliu, TN1-NPGRC, TN1-TDARES, and TN1-NTU.
DOI: 10.6084/m9.figshare.9751211
title: Additional file 10: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs in JS1-3 vs. FM1-3.(XLSX 11 kb)
DOI: 10.6084/m9.figshare.9751211.v1
title: Additional file 10: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs in JS1-3 vs. FM1-3.(XLSX 11 kb)
DOI: 10.6084/m9.figshare.9751217
title: Additional file 11: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The genes that regulate the development and quantitative variation of carpels in A. thaliana.(XLSX 10 kb)
DOI: 10.6084/m9.figshare.9751217.v1
title: Additional file 11: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The genes that regulate the development and quantitative variation of carpels in A. thaliana.(XLSX 10 kb)
DOI: 10.6084/m9.figshare.9751232
title: Additional file 13: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs in greenyellow, lightcyan and pink modules.(XLSX 12 kb)
DOI: 10.6084/m9.figshare.9751232.v1
title: Additional file 13: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs in greenyellow, lightcyan and pink modules.(XLSX 12 kb)
DOI: 10.6084/m9.figshare.9751241
title: Additional file 14: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: Primers for qRT-PCR analysis.(XLSX 10 kb)
DOI: 10.6084/m9.figshare.9751241.v1
title: Additional file 14: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: Primers for qRT-PCR analysis.(XLSX 10 kb)
DOI: 10.6084/m9.figshare.9751256
title: Additional file 1: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: Throughput and quality of next-generation and single-molecule long-read RNA-seq.(XLSX 12 kb)
DOI: 10.6084/m9.figshare.9751256.v1
title: Additional file 1: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: Throughput and quality of next-generation and single-molecule long-read RNA-seq.(XLSX 12 kb)
DOI: 10.6084/m9.figshare.14994155
title: Relationship between diagnostic accuracy of microRNAs for NSCLC and number of combined microRNAs: an overview with meta-analysis

description: <b>Objective</b>: Several systematic reviews (SRs) have assessed the diagnostic accuracy of microRNAs (miRNAs) for NSCLC, and this overview aimed to assess the relationship between diagnostic accuracy of miRNAs for NSCLC and number of microRNAs combinations. <b>Methods</b>: Embase.com, PubMed, the Cochrane Library, and Web of Science were searched. The PRISMA-DTA was used for reporting quality evaluation. Meta-analysis was conducted to assess the pooled diagnostic accuracy of different miRNAs combinations, and subgroup analyses were performed based on the source of miRNA. <b>Results</b>: Fourteen SRs with 91 original studies were included. Three SRs had minimal reporting flaws, and 11 SRs had medium flaws. The pooled sensitivity and specificity were 0.76 and 0.80 for single miRNA, 0.80 and 0.81 for two miRNAs combined, 0.82 and 0.88 for three miRNAs combined, 0.88 and 0.92 for four miRNAs combined, 0.87 and 0.87 for five miRNAs combined, and 0.87 and 0.89 for six or more miRNAs combined. And miR-21 was mostly appeared. Subgroup analyses suggested that the serum-derived miRNA had the relatively best diagnostic value compared to other sources. <b>Conclusions</b>: Future studies should explore specific and serum-derived miRNAs in NSCLC and combine them to improve the diagnosis accuracy of NSCLC, which had great significance in economic efficiency.
DOI: 10.6084/m9.figshare.20236154
title: Additional file 2 of Integrated analysis reveals the dysfunction of signaling pathways in uveal melanoma

description: Additional file 2: Table_S2. Clinical information and gene-expression profile of the three primary uveal melanomas
DOI: 10.6084/m9.figshare.20236166.v1
title: Additional file 6 of Integrated analysis reveals the dysfunction of signaling pathways in uveal melanoma

description: Additional file 6: Table_S6. Differentially expressed genes in each cluster
DOI: 10.6084/m9.figshare.20236163.v1
title: Additional file 5 of Integrated analysis reveals the dysfunction of signaling pathways in uveal melanoma

description: Additional file 5: Table_S5. Differentially expressed genes in TCGA data_UVM
DOI: 10.6084/m9.figshare.9751289
title: Additional file 6: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs of significant enrichment patterns (profile 6, profile14 and profile 41) in FM cultivar.(XLSX 12 kb)
DOI: 10.6084/m9.figshare.9751289.v1
title: Additional file 6: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs of significant enrichment patterns (profile 6, profile14 and profile 41) in FM cultivar.(XLSX 12 kb)
DOI: 10.6084/m9.figshare.20236166
title: Additional file 6 of Integrated analysis reveals the dysfunction of signaling pathways in uveal melanoma

description: Additional file 6: Table_S6. Differentially expressed genes in each cluster
DOI: 10.6084/m9.figshare.20236151
title: Additional file 1 of Integrated analysis reveals the dysfunction of signaling pathways in uveal melanoma

description: Additional file 1: Table_S1. Summary information for the 4 original scRNA-seq datasets and integrated dataset
DOI: 10.6084/m9.figshare.9751301
title: Additional file 9: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs in JS vs. FM combinations.(XLSX 11 kb)
DOI: 10.6084/m9.figshare.9751301.v1
title: Additional file 9: of Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii

description: The DEGs in JS vs. FM combinations.(XLSX 11 kb)
DOI: 10.6084/m9.figshare.9751304
title: Additional file 1: of Tac2-N acts as a novel oncogene and promotes tumor metastasis via activation of NF-κB signaling in lung cancer

description: Figure S1. TC2N promotes lung and liver metastasis of lung cancer cells in nude mice. a, b Liver metastases were observed by H&E staining. c, d Lung and liver metastasis were further quantified using RT-qPCR. Human-specific β2-MG levels were used to quantify metastatic human cancer cells with the mouse-specific β2-MG level as an internal control. Error bars indicate s.d. (n = 4).*P &lt; 0.05. Figure S2. Ectopic expression of TC2N does not affected the NF-κB mRNA expression. a The mRNA expression of p65 and p50 were examined by qRT–PCR after reexpression of TC2N in H1975 cells. b The mRNA expression of p65 and p50 were examined by qRT–PCR after knockdown of TC2N in H1299 cells. ACTIN serves as an internal control. Table S1. The primer applied in the study. (ZIP 1723 kb)
DOI: 10.6084/m9.figshare.9751304.v1
title: Additional file 1: of Tac2-N acts as a novel oncogene and promotes tumor metastasis via activation of NF-κB signaling in lung cancer

description: Figure S1. TC2N promotes lung and liver metastasis of lung cancer cells in nude mice. a, b Liver metastases were observed by H&E staining. c, d Lung and liver metastasis were further quantified using RT-qPCR. Human-specific β2-MG levels were used to quantify metastatic human cancer cells with the mouse-specific β2-MG level as an internal control. Error bars indicate s.d. (n = 4).*P &lt; 0.05. Figure S2. Ectopic expression of TC2N does not affected the NF-κB mRNA expression. a The mRNA expression of p65 and p50 were examined by qRT–PCR after reexpression of TC2N in H1975 cells. b The mRNA expression of p65 and p50 were examined by qRT–PCR after knockdown of TC2N in H1299 cells. ACTIN serves as an internal control. Table S1. The primer applied in the study. (ZIP 1723 kb)
DOI: 10.6084/m9.figshare.14994189
title: Serum macrophage inhibitory cytokine-1 serves as a novel diagnostic biomarker of early-stage colorectal cancer

description: Patients with colorectal cancer usually have a poor prognosis because of the absence of suitable biomarkers for diagnosing asymptomatic patients. Here we determined the ability of MIC-1 to detect precancerous lesions and CRC in an asymptomatic cohort from CRC Screening Program. We screened 2759 subjects with risk factors. Endoscopic and histopathological analyses revealed that 19 and 47 subjects had CRC or precancerous lesions. We randomly selected 24 subjects with normal colonoscopies as healthy controls. We used receiver operating characteristic curve analysis to evaluate the diagnostic efficacy of MIC-1 for CRC and precancerous lesions. The optimal thresholds of MIC-1 levels with precancerous lesions or CRC were 314.12 pg/mL (sensitivity, 91.50%; specificity, 54.20%) and 357.64 pg/mL (sensitivity, 82.40%; specificity, 70.80%). Moreover, MIC-1 levels distinguished precancerous lesions better than CEA, CA19-9, or CA24-2 (AUC: 0.760 <i>vs.</i> 0.529, 0.624, and 0.585) or CRC (AUCs: 0.821 <i>vs.</i> 0.743, 0.657, and 0.688) from the healthy controls. The combination of MIC-1, CEA, CA19-9, and CA24-2 showed the highest in sensitivity and specificity for CRC diagnosis (sensitivity, 94.10%; specificity, 87.50%). Serum MIC-1 levels increased the sensitivity of detection of precancerous colorectal lesions and CRC and can be used to improve screening.
DOI: 10.6084/m9.figshare.20237069
title: Recombinant human granulocyte colony stimulating factor (rhG-CSF) participates in the progression of implantation via the hsa_circ_0001550-miRNA-mRNA interaction network

description: Inadequate endometrial receptivity is a key factor affecting the successful implantation of embryos. Recombinant human granulocyte colony stimulating factor (rhG-CSF) can increase endometrial thickness and improve the outcomes of assisted reproductive technologies (ARTs). In this preliminary study, the function and possible molecular mechanisms of recombinant human granulocyte colony stimulating factor (rhG-CSF) which affects endometrial receptivity and implantation in human Embryonic Stem Cells (hESCs) were investigated. The cell viability of endometrial stromal cells treated with rhG-CSF 0.5 ng/ml for 24 h was significantly increased. Moreover, the expression of hsa_circ_0001550 was downregulated in endometrial stromal cells treated with rhG-CSF. Furthermore, the hsa_circ_0001550-miRNA-mRNA network was constructed and the downstream target genes (including 4 miRNAs and 117 mRNAs) of hsa_circ_0001550 were mainly involved in the cAMP and calcium signalling pathways, which play important roles in regulating endometrial receptivity and embryo implantation. We conclude that rhG-CSF participates in the regulation of embryo implantation by regulating the hsa_circ_0001550-miRNA-mRNA interaction network.
DOI: 10.6084/m9.figshare.20237069.v1
title: Recombinant human granulocyte colony stimulating factor (rhG-CSF) participates in the progression of implantation via the hsa_circ_0001550-miRNA-mRNA interaction network

description: Inadequate endometrial receptivity is a key factor affecting the successful implantation of embryos. Recombinant human granulocyte colony stimulating factor (rhG-CSF) can increase endometrial thickness and improve the outcomes of assisted reproductive technologies (ARTs). In this preliminary study, the function and possible molecular mechanisms of recombinant human granulocyte colony stimulating factor (rhG-CSF) which affects endometrial receptivity and implantation in human Embryonic Stem Cells (hESCs) were investigated. The cell viability of endometrial stromal cells treated with rhG-CSF 0.5 ng/ml for 24 h was significantly increased. Moreover, the expression of hsa_circ_0001550 was downregulated in endometrial stromal cells treated with rhG-CSF. Furthermore, the hsa_circ_0001550-miRNA-mRNA network was constructed and the downstream target genes (including 4 miRNAs and 117 mRNAs) of hsa_circ_0001550 were mainly involved in the cAMP and calcium signalling pathways, which play important roles in regulating endometrial receptivity and embryo implantation. We conclude that rhG-CSF participates in the regulation of embryo implantation by regulating the hsa_circ_0001550-miRNA-mRNA interaction network.
DOI: 10.6084/m9.figshare.9751325
title: Additional file 10: of Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice

description: Detection of fusion genes. Table S11. All detected fusion genesâ sequences. Table S12. Positions of 915 fusion genes. (XLSX 1247 kb)