cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.18393566.v1
title: Additional file 5 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 5: Table S3: Average proportions of 22 immune cells subsets in GSE135820-HGSOC, GETx-Normal, Serous, Endometrioid, Clear cell, and TCGA-OC databases. GTEx, Genotype-Tissue Expression; HGSOC, High-grade serous ovarian carcinoma; OC, Ovarian cancer; TCGA, The Cancer General Atlas
DOI: 10.6084/m9.figshare.18393560
title: Additional file 3 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 3: Table S1: Clinical data for sample id, overall survival time, survival state, and the average expression of PD-1/PD-L1 in GSE53963, GSE32062, GSE135820, and TCGA-OV databases. PD-1, programmed death-1; PD-L1, programmed death ligand 1; TCGA, The Cancer General Atlas
DOI: 10.6084/m9.figshare.18393560.v1
title: Additional file 3 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 3: Table S1: Clinical data for sample id, overall survival time, survival state, and the average expression of PD-1/PD-L1 in GSE53963, GSE32062, GSE135820, and TCGA-OV databases. PD-1, programmed death-1; PD-L1, programmed death ligand 1; TCGA, The Cancer General Atlas
DOI: 10.6084/m9.figshare.18393572.v1
title: Additional file 7 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 7: Table S5: Correlation between overall survival of 239 HGSOC patients and the content of APC infiltrating cells (M1 macrophages, dendritic cells, and B cells).
DOI: 10.6084/m9.figshare.18393563.v1
title: Additional file 4 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 4: Table S2: Proportions of infiltrating immune cells of each sample in GSE53963, GSE32062, GSE135820, GSE17260, GSE73614, GSE68600, GSE73638, TCGA-OC, and GETx databases. GTEx, Genotype-Tissue Expression; OC, Ovarian cancer; TCGA, The Cancer General Atlas
DOI: 10.6084/m9.figshare.18393566
title: Additional file 5 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 5: Table S3: Average proportions of 22 immune cells subsets in GSE135820-HGSOC, GETx-Normal, Serous, Endometrioid, Clear cell, and TCGA-OC databases. GTEx, Genotype-Tissue Expression; HGSOC, High-grade serous ovarian carcinoma; OC, Ovarian cancer; TCGA, The Cancer General Atlas
DOI: 10.6084/m9.figshare.18393569
title: Additional file 6 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 6: Table S4: Immune cells could be classified into three optimal cluster groups in 2873 HGSOC samples with CIBERSORT: cluster 1/A (n = 1961), cluster 2/B (n = 737), and cluster 3/C (n = 175). HGSOC, High-grade serous ovarian carcinoma
DOI: 10.6084/m9.figshare.18393569.v1
title: Additional file 6 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 6: Table S4: Immune cells could be classified into three optimal cluster groups in 2873 HGSOC samples with CIBERSORT: cluster 1/A (n = 1961), cluster 2/B (n = 737), and cluster 3/C (n = 175). HGSOC, High-grade serous ovarian carcinoma
DOI: 10.6084/m9.figshare.17870076
title: Additional file 6 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 6: Table S5. GO classification of host genes for DE-circRNAs.
DOI: 10.6084/m9.figshare.18393572
title: Additional file 7 of Combined PD-1/PD-L1 and tumor-infiltrating immune cells redefined a unique molecular subtype of high-grade serous ovarian carcinoma

description: Additional file 7: Table S5: Correlation between overall survival of 239 HGSOC patients and the content of APC infiltrating cells (M1 macrophages, dendritic cells, and B cells).
DOI: 10.6084/m9.figshare.14726918
title: RaSE: A Variable Screening Framework via Random Subspace Ensembles

description: Variable screening methods have been shown to be effective in dimension reduction under the ultra-high dimensional setting. Most existing screening methods are designed to rank the predictors according to their individual contributions to the response. As a result, variables that are marginally independent but jointly dependent with the response could be missed. In this work, we propose a new framework for variable screening, <i>random subspace ensemble (RaSE)</i>, which works by evaluating the quality of random subspaces that may cover multiple predictors. This new screening framework can be naturally combined with any subspace evaluation criterion, which leads to an array of screening methods. The framework is capable to identify signals with no marginal effect or with high-order interaction effects. It is shown to enjoy the sure screening property and rank consistency. We also develop an iterative version of RaSE screening with theoretical support. Extensive simulation studies and real-data analysis show the effectiveness of the new screening framework.
DOI: 10.6084/m9.figshare.14199520.v1
title: Estimation and Inference for Multi-Kink Quantile Regression

description: This article proposes a new Multi-Kink Quantile Regression (MKQR) model which assumes different linear quantile regression forms in different regions of the domain of the threshold covariate but are still continuous at kink points. First, we investigate parameter estimation, kink points detection and statistical inference in MKQR models. We propose an iterative segmented quantile regression algorithm for estimating both the regression coefficients and the locations of kink points. The proposed algorithm is much more computationally efficient than the grid search algorithm and not sensitive to the selection of initial values. Second, asymptotic properties, such as selection consistency of the number of kink points and asymptotic normality of the estimators of both regression coefficients and kink effects, are established to justify the proposed method theoretically. Third, a score test based on partial subgradients is developed to verify whether the kink effects exist or not. Test-inversion confidence intervals for kink location parameters are also constructed. Monte Carlo simulations and two real data applications on the secondary industrial structure of China and the triceps skinfold thickness of Gambian females illustrate the excellent finite sample performances of the proposed MKQR model. A new R package <i>MultiKink</i> is developed to easily implement the proposed methods.
DOI: 10.6084/m9.figshare.24164109
title: A Modified Randomization Test for the Level of Clustering

description: Suppose a researcher observes individuals within a county within a state. Given concerns about correlation across individuals, it is common to group observations into clusters and conduct inference treating observations across clusters as independent. However, a researcher that has chosen to cluster at the county level may be unsure of their decision, given knowledge that observations are independent across states. This article proposes a modified randomization test as a robustness check for the chosen level of clustering in a linear regression setting. Existing tests require either the number of states or number of counties to be large. Our method is designed for settings with few states and few counties. While the method is conservative, it has competitive power in settings that may be relevant to empirical work.
DOI: 10.6084/m9.figshare.17869935.v1
title: Additional file 12 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 12.
DOI: 10.6084/m9.figshare.24164109.v1
title: A Modified Randomization Test for the Level of Clustering

description: Suppose a researcher observes individuals within a county within a state. Given concerns about correlation across individuals, it is common to group observations into clusters and conduct inference treating observations across clusters as independent. However, a researcher that has chosen to cluster at the county level may be unsure of their decision, given knowledge that observations are independent across states. This article proposes a modified randomization test as a robustness check for the chosen level of clustering in a linear regression setting. Existing tests require either the number of states or number of counties to be large. Our method is designed for settings with few states and few counties. While the method is conservative, it has competitive power in settings that may be relevant to empirical work.
DOI: 10.6084/m9.figshare.12102435.v1
title: Genome-wide assessment of population structure and genetic diversity for <i>Anabasis aphylla</i> based on specific length amplification fragment sequencing

description: <i>Anabasis aphylla</i> is a salt and alkali resistant shrub grows in arid and semi-arid areas, which is also a constructive species of desert soil. To reveal the population structure and genetic diversity in populations of <i>A. aphylla</i>, a total of 106 samples were used as experimental materials for sequencing by specific-locus amplified fragment sequencing. In total, we obtained 300105 SNP which had high consistency. Phylogenetic tree of <i>A. aphylla</i> result showed there was a certain difference between these samples, which can be divided into two groups. The Shanon–Wiener index of <i>A. aphylla</i> was 0.4440 and the Nei diversity index was 0.2854. AMOVA analysis showed there was genetic differentiation among the seven groups to a certain level. The genetic diversity analysis showed the genetic variation of <i>A. aphylla</i> mainly from groups. This study provides a reference for further comprehensive study of the genetic structure and evolutionary adaptation of <i>A. aphylla</i>.
DOI: 10.6084/m9.figshare.8956700.v1
title: Autophagy induction by the pathogen receptor NECTIN4 and sustained autophagy contribute to peste des petits ruminants virus infectivity

description: Macroautophagy/autophagy is an essential cellular response in the fight against intracellular pathogens. Although some viruses can escape from or utilize autophagy to ensure their own replication, the responses of autophagy pathways to viral invasion remain poorly documented. Here, we show that peste des petits ruminants virus (PPRV) infection induces successive autophagic signalling in host cells via distinct and uncoupled molecular pathways. Immediately upon invasion, PPRV induced a first transient wave of autophagy via a mechanism involving the cellular pathogen receptor NECTIN4 and an AKT-MTOR-dependent pathway. Autophagic detection showed that early PPRV infection not only increased the amounts of autophagosomes and LC3-II but also downregulated the phosphorylation of AKT-MTOR. Subsequently, we found that the binding of viral protein H to NECTIN4 ultimately induced a wave of autophagy and inactivated the AKT-MTOR pathway, which is a critical step for the control of infection. Soon after infection, new autophagic signalling was initiated that required viral replication and protein expression. Interestingly, expression of IRGM and HSPA1A was significantly upregulated following PPRV replication. Strikingly, knockdown of IRGM and HSPA1A expression using small interfering RNAs impaired the PPRV-induced second autophagic wave and viral particle production. Moreover, IRGM-interacting PPRV-C and HSPA1A-interacting PPRV-N expression was sufficient to induce autophagy through an IRGM-HSPA1A-dependent pathway. Importantly, syncytia formation could facilitate sustained autophagy and the replication of PPRV. Overall, our work reveals distinct molecular pathways underlying the induction of self-beneficial sustained autophagy by attenuated PPRV, which will contribute to improving the use of vaccines for therapy. <b>Abbreviations:</b> ACTB: actin beta; ANOVA: analysis of variance; ATG: autophagy-related; BECN1: beclin 1; CDV: canine distemper virus; Co-IP: coimmunoprecipitation; FIP: fusion inhibitory peptide; GFP: green fluorescent protein; GST: glutathione S-transferase; HMOX1: heme oxygenase 1; hpi: hours post infection; HSPA1A: heat shock protein family A (Hsp70) member 1A; HSP90AA1: heat shock protein 90 kDa alpha (cytosolic), class A member 1; IFN: interferon; IgG: immunoglobulin G; INS: insulin; IRGM: immunity related GTPase M; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MeV: measles virus; MOI: multiplicity of infection; MTOR: mechanistic target of rapamycin kinase; PI3K: phosphoinositide-3 kinase; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; SDS: sodium dodecyl sulfate; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; UV: ultraviolet.
DOI: 10.6084/m9.figshare.17869962
title: Additional file 9 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 9.
DOI: 10.6084/m9.figshare.17870058
title: Additional file 14 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 14: Table S13. Primers used in this study.
DOI: 10.6084/m9.figshare.17870070.v1
title: Additional file 4 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 4: Table S3. GO classification of host genes for all the identified circRNAs.
DOI: 10.6084/m9.figshare.17870079.v1
title: Additional file 7 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 7: Table S6. KEGG pathways analysis of host genes for DE-circRNAs.
DOI: 10.6084/m9.figshare.12102792.v1
title: Layered bifuncational Co(II) coordination polymer for photodegradation of organic dyes and anti-osteoporosis activity by activating wnt/β-catenin/PPARγ pathway in BMSCs

description: A new coordination polymer (CP) [Co(HTATB)(H<sub>2</sub>O)](DMF)<sub>2</sub> (<b>1</b>, DMF = N,N-dimethylformamide) based on the {Co<sub>2</sub>(CO<sub>2</sub>)<sub>4</sub>} binuclear secondary building unit (SBU) has been successfully prepared by using a light-harvesting triphenylamine type organic ligand 4,4′,4″-s-triazine-2,4,6-triyltribenzoic acid (H<sub>3</sub>TATB). Furthermore, complex <b>1</b> has significant photocatalytic activity under visible light for the degradation of organic dyes such as rhodamine B (RhB), methylene blue (MB) as well as methyl orange (MO) assisted by H<sub>2</sub>O<sub>2</sub>. Furthermore, the anti-osteoporosis activity of complex <b>1</b> was evaluated. First, the inhibitory effect of complex <b>1</b> on the BMSCs apoptosis was measured by Annexin V-FITC/PI method. Then, the RT-PCR was performed to detect the relative expressions level of wnt/β-catenin and PPARγ after complex <b>1</b> treatment. The hypothesis that arises from the experimental observation has been further investigated by using molecular docking simulation, where the possible binding interactions between the ligand and Wnt protein are studied explicitly.
DOI: 10.6084/m9.figshare.17870082.v1
title: Additional file 8 of Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages

description: Additional file 8: Table S7. CircRNA AS events identified in T. rubrum conidial and mycelial stages.
DOI: 10.6084/m9.figshare.17869995.v1
title: Additional file 16 of Gene regulation network analyses of pistil development in papaya

description: Additional file 16. Summary statistics of RNA-Seq data from papaya male and female flowers.
DOI: 10.6084/m9.figshare.17869998
title: Additional file 17 of Gene regulation network analyses of pistil development in papaya

description: Additional file 17. Primer information used for RT-qPCR experimental verification in this study. Primers CpHEC2, CpSUPL, and CpAGL11 are used to verify the false positive of RNA-seq differential expression analysis. FS and MS primers are used to verify the false positives of the female and male preferential expression algorithm, respectively.
DOI: 10.6084/m9.figshare.17870007.v1
title: Additional file 3 of Gene regulation network analyses of pistil development in papaya

description: Additional file 3. Statistics of genes preferentially expressed by different sexes at different developmental stages.
DOI: 10.6084/m9.figshare.17869929
title: Additional file 10 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 10.
DOI: 10.6084/m9.figshare.17869935
title: Additional file 12 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 12.
DOI: 10.6084/m9.figshare.17869929.v1
title: Additional file 10 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 10.
DOI: 10.6084/m9.figshare.17869932.v1
title: Additional file 11 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 11.
DOI: 10.6084/m9.figshare.17869944.v1
title: Additional file 3 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 3.
DOI: 10.6084/m9.figshare.17869947
title: Additional file 4 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 4.
DOI: 10.6084/m9.figshare.6338327.v1
title: Additional file 1 of Investigation of the thermophilic mechanism in the genus Porphyrobacter by comparative genomic analysis

description: Alignment results of protein amino acid sequences encoded by single-copy genes found in eight Porphyrobacter strains. (ZIP 1510 kb)
DOI: 10.6084/m9.figshare.17870202
title: Additional file 7 of An 8-ferroptosis-related genes signature from Bronchoalveolar Lavage Fluid for prognosis in patients with idiopathic pulmonary fibrosis

description: Additional file 7: Table S1. The 293 ferroptosis-related genes used in the study.
DOI: 10.6084/m9.figshare.17869953
title: Additional file 6 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 6.
DOI: 10.6084/m9.figshare.12623243
title: Additional file 1 of Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid

description: Additional file 1 Table S1. List of tRFs identified in this study and their expression levels. Table S2. The differential expression levels in the control (C1D) and ABA-treatment (A1D) libraries of tRFs after reducing noise. Table S3. List of differentially expressed tRFs with a minimum 10 RPM value in one library. Table S4. List of phasiRNAs identified in this study and their expression levels. Table S5. The differential expression levels in the control (C1D) and ABA-treatment (A1D) libraries of phasiRNAs. Table S6. List of differentially expressed phasiRNAs with a minimum 10 RPM value in one library. Table S7. The target genes of phasiRNAs. Table S8. The expression patterns of phasiRNAs targets
DOI: 10.6084/m9.figshare.6338354.v1
title: Additional file 3: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

description: Table S2. DEGs identified in liver of E12 embryos between the fat and lean lines. (XLSX 27Â kb)
DOI: 10.6084/m9.figshare.12623243.v1
title: Additional file 1 of Identification of tRFs and phasiRNAs in tomato (Solanum lycopersicum) and their responses to exogenous abscisic acid

description: Additional file 1 Table S1. List of tRFs identified in this study and their expression levels. Table S2. The differential expression levels in the control (C1D) and ABA-treatment (A1D) libraries of tRFs after reducing noise. Table S3. List of differentially expressed tRFs with a minimum 10 RPM value in one library. Table S4. List of phasiRNAs identified in this study and their expression levels. Table S5. The differential expression levels in the control (C1D) and ABA-treatment (A1D) libraries of phasiRNAs. Table S6. List of differentially expressed phasiRNAs with a minimum 10 RPM value in one library. Table S7. The target genes of phasiRNAs. Table S8. The expression patterns of phasiRNAs targets
DOI: 10.6084/m9.figshare.17869920.v1
title: Additional file 2 of Biochemical and transcriptomic analyses of the symbiotic interaction between Cremastra appendiculata and the mycorrhizal fungus Coprinellus disseminatus

description: Additional file 2: Table S1. Overview of transcriptome sequence and de novo assembly results. Table S2. Overview of transcriptome assembly showing length of CDS and unigenes. Table S3. Summary of functional annotation of contigs from BLAST searches against public databases. Table S4. DEGs richment (log2 FC ≥ 2, Qvalue≤0.05). Table S5. Significantly overrepresented gene ontology terms during the symbiotic germination of C. appendiculata with C. disseminatus DJF-10. Table S6. Significantly enriched KEGG pathway of different samples. Table S7. DEGs enrichment of KEGG during symbiotic germination. Table S8. DEGs related to water and ABA biosynthesis.
DOI: 10.6084/m9.figshare.17869932
title: Additional file 11 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 11.
DOI: 10.6084/m9.figshare.17869944
title: Additional file 3 of Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam

description: Additional file 3.
DOI: 10.6084/m9.figshare.17869980.v1
title: Additional file 11 of Gene regulation network analyses of pistil development in papaya

description: Additional file 11. Statistics of topological attribute information of different gene regulatory networks.
DOI: 10.6084/m9.figshare.17869920
title: Additional file 2 of Biochemical and transcriptomic analyses of the symbiotic interaction between Cremastra appendiculata and the mycorrhizal fungus Coprinellus disseminatus

description: Additional file 2: Table S1. Overview of transcriptome sequence and de novo assembly results. Table S2. Overview of transcriptome assembly showing length of CDS and unigenes. Table S3. Summary of functional annotation of contigs from BLAST searches against public databases. Table S4. DEGs richment (log2 FC ≥ 2, Qvalue≤0.05). Table S5. Significantly overrepresented gene ontology terms during the symbiotic germination of C. appendiculata with C. disseminatus DJF-10. Table S6. Significantly enriched KEGG pathway of different samples. Table S7. DEGs enrichment of KEGG during symbiotic germination. Table S8. DEGs related to water and ABA biosynthesis.