cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16958638
title: Test of Weak Separability for Spatially Stationary Functional Field

description: For spatially dependent functional data, a generalized Karhunen-Loève expansion is commonly used to decompose data into an additive form of temporal components and spatially correlated coefficients. This structure provides a convenient model to investigate the space-time interactions, but may not hold for complex spatio-temporal processes. In this work, we introduce the concept of weak separability, and propose a formal test to examine its validity for non-replicated spatially stationary functional field. The asymptotic distribution of the test statistic that adapts to potentially diverging ranks is derived by constructing lag covariance estimation, which is easy to compute for practical implementation. We demonstrate the efficacy of the proposed test via simulations and illustrate its usefulness in two real examples: China PM 2.5 data and Harvard Forest data. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.8045813
title: Additional file 4: of The trihelix family of transcription factors: functional and evolutionary analysis in Moso bamboo (Phyllostachys edulis)

description: Table S3. Promoter analysis of TTF proteins in Moso bamboo. (XLS 50 kb)
DOI: 10.6084/m9.figshare.8045747
title: Additional file 2: of The high-affinity transporter BnPHT1;4 is involved in phosphorus acquisition and mobilization for facilitating seed germination and early seedling growth of Brassica napus

description: Dataset S1. Dynamics of the relative pool sizes (%) of the total phosphorus (P) in the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown under 1 mM Pi. Dataset S2. Dynamics of the relative pool sizes (%) of the total phosphorus (P) in the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown without Pi. Dataset S3. Quantitative analysis of germination rates of the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown on 1/2 MS medium with 10, 50 and 100 μM abscisic acid (ABA). Dataset S4. Quantitative analysis of germination rates of the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown on 1/2 MS medium with 100 μM gibberellins (GA) or 10 mM paclobutrazol (PAC). (XLS 51 kb)
DOI: 10.6084/m9.figshare.8045747.v1
title: Additional file 2: of The high-affinity transporter BnPHT1;4 is involved in phosphorus acquisition and mobilization for facilitating seed germination and early seedling growth of Brassica napus

description: Dataset S1. Dynamics of the relative pool sizes (%) of the total phosphorus (P) in the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown under 1 mM Pi. Dataset S2. Dynamics of the relative pool sizes (%) of the total phosphorus (P) in the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown without Pi. Dataset S3. Quantitative analysis of germination rates of the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown on 1/2 MS medium with 10, 50 and 100 μM abscisic acid (ABA). Dataset S4. Quantitative analysis of germination rates of the BnPHT1;4 overexpression transgenic seedlings of Brassica napus grown on 1/2 MS medium with 100 μM gibberellins (GA) or 10 mM paclobutrazol (PAC). (XLS 51 kb)
DOI: 10.6084/m9.figshare.8045762.v1
title: Additional file 2: of Characterization of an NDM-5 carbapenemase-producing Escherichia coli ST156 isolate from a poultry farm in Zhejiang, China

description: Table S4. The information for the blaNDM-harboring plasmids with complete sequences in China. (XLSX 20 kb)
DOI: 10.6084/m9.figshare.8045762
title: Additional file 2: of Characterization of an NDM-5 carbapenemase-producing Escherichia coli ST156 isolate from a poultry farm in Zhejiang, China

description: Table S4. The information for the blaNDM-harboring plasmids with complete sequences in China. (XLSX 20 kb)
DOI: 10.17617/4.eh
title: Topology sorting: Separating linear/star polymer blend components by imbibition in nanopores

description: Kardasis, P., Tzourtzouklis, I., Nega, A. D., Sakellariou, G., Steinhart, M., & Floudas, G. (2024). Topology sorting: Separating linear/star polymer blend components by imbibition in nanopores. The Journal of Chemical Physics, 160(4): 044912. doi:10.1063/5.0189661.
DOI: 10.6084/m9.figshare.25163672
title: Supplementary Data 1 - 20

description: Biocontrol strategies offer a promising alternative to control plant pathogens achieving food safety and security. In this study we apply a RNAseq analysis during interaction between the biocontrol agent (BCA) <i>Papiliotrema terrestris</i>, the pathogen <i>Penicillium expansum</i>, and the host <i>Malus domestica</i>. Analysis of the BCA finds overall 802 upregulated DEGs (differentially expressed genes) when grown in apple tissues, with the majority being involved in nutrients uptake and oxidative stress response. This suggests that these processes are crucial for the BCA to colonize the fruit wounds and outcompete the pathogen. As to <i>P. expansum</i> analysis, 1017 DEGs are upregulated when grown in apple tissues, with the most represented GO categories being transcription, oxidation reduction process, and transmembrane transport. Analysis of the host <i>M. domestica</i> finds a higher number of DEGs in response to the pathogen compared to the BCA, with overexpression of genes involved in host defense signaling pathways in the presence of both of them, and a prevalence of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) only during interaction with <i>P. expansum</i>. This analysis contributes to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.<br>
DOI: 10.6084/m9.figshare.25163672.v1
title: Supplementary Data 1 - 20

description: Biocontrol strategies offer a promising alternative to control plant pathogens achieving food safety and security. In this study we apply a RNAseq analysis during interaction between the biocontrol agent (BCA) <i>Papiliotrema terrestris</i>, the pathogen <i>Penicillium expansum</i>, and the host <i>Malus domestica</i>. Analysis of the BCA finds overall 802 upregulated DEGs (differentially expressed genes) when grown in apple tissues, with the majority being involved in nutrients uptake and oxidative stress response. This suggests that these processes are crucial for the BCA to colonize the fruit wounds and outcompete the pathogen. As to <i>P. expansum</i> analysis, 1017 DEGs are upregulated when grown in apple tissues, with the most represented GO categories being transcription, oxidation reduction process, and transmembrane transport. Analysis of the host <i>M. domestica</i> finds a higher number of DEGs in response to the pathogen compared to the BCA, with overexpression of genes involved in host defense signaling pathways in the presence of both of them, and a prevalence of pattern-triggered immunity (PTI) and effector-triggered immunity (ETI) only during interaction with <i>P. expansum</i>. This analysis contributes to advance the knowledge on the molecular mechanisms that underlie biocontrol activity and the tritrophic interaction of the BCA with the pathogen and the host.<br>
DOI: 10.6084/m9.figshare.8045870.v1
title: Additional file 4: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Figure S1. The sequence alignment of the conserved domain (bZIP domain) in ItbZIP transcription factors. The primary structure of the bZIP domain and highly conserved residues of the bZIP domain consensus sequence [N-X7-R/K-X9-L-X6-L-X6-L] are shown at the top of the picture. Vertical bars with different colors on the left show different subfamilies. The black and gray shades in the picture present the same and similar amino acids, respectively. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8045900.v1
title: Additional file 6: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S5. Relative expression levels of ItfbZIPs in various tissues. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.8045849
title: Additional file 2: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S2. Distribution of bZIP transcription factors in eukaryotes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8045888.v1
title: Additional file 5: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S4. Cis-elements associated with abiotic stress in promoter region of ItfbZIPs. (XLS 38 kb)
DOI: 10.6084/m9.figshare.8045861.v1
title: Additional file 3: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S3. Accession numbers of bZIP genes in Ipomoea trifida, Arabidopsis thaliana and Solanum lycopersicum. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8045918.v1
title: Additional file 8: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S7. Primers of the ItfbZIP genes and housekeeping gene for qRT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8045843
title: Additional file 1: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S1. Chromosomal locations and segmental duplication of ItfbZIP genes. (EMF 15058 kb)
DOI: 10.6084/m9.figshare.8045900
title: Additional file 6: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S5. Relative expression levels of ItfbZIPs in various tissues. (XLSX 30 kb)
DOI: 10.6084/m9.figshare.10041107
title: Additional file 6: of Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis

description: Table S1 Full statistical comparison of data in Fig.Â 7. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.10041107.v1
title: Additional file 6: of Protein recoding by ADAR1-mediated RNA editing is not essential for normal development and homeostasis

description: Table S1 Full statistical comparison of data in Fig.Â 7. (XLSX 120 kb)
DOI: 10.6084/m9.figshare.10041113
title: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

description: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
DOI: 10.6084/m9.figshare.10041113.v1
title: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

description: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
DOI: 10.6084/m9.figshare.7527764
title: Porous hypercrosslinked polymer-TiO2-graphene composite photocatalysts for visible-light-driven CO2 conversion

description: <b>The data supporting the plots
within this paper and other findings of this study are available from the
corresponding author on request. The
source data underlying Figs 3a-f and 4a–e and Supplementary Figs 7-12, 14,16,
18-23, 25-30 and 32-40 are provided as a Source Data file.</b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.24305026
title: Renal and cardiac effects of the PDE9 inhibitor BAY 73-6691 in 5/6 nephrectomized rats.

description: We examined the effects of the PDE9 inhibitor BAY 73-6691 on the kidney and heart for the first time in a 5/6 nephrectomy animal model using BAY 73-6691 dosages known to be effective in other rat disease models. We did not observe any relevant effects of the PDE9 inhibitor BAY 73-6691 on renal function, renal histology, and renal disease-related pathways and gene expression in 5/6 nephrectomy rats. In addition, the effects of the PDE9 inhibitor BAY 73-6691 on the heart of 5/6 nephrectomy rats were mild. Except for cardiomyocyte size, BAY 73-6691 had no effect on other cardiac histological parameters, cardiac function, and disease-related genes and pathways.
DOI: 10.6084/m9.figshare.8045912.v1
title: Additional file 7: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S6. Expression pattern of ItfbZIPs under abiotic stresses. (XLSX 38 kb)
DOI: 10.21253/dmu.25205603
title: Template for Participant demographics

description: Template for Participant demographics.
DOI: 10.21253/dmu.25205603.v1
title: Template for Participant demographics

description: Template for Participant demographics.
DOI: 10.6084/m9.figshare.8045870
title: Additional file 4: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Figure S1. The sequence alignment of the conserved domain (bZIP domain) in ItbZIP transcription factors. The primary structure of the bZIP domain and highly conserved residues of the bZIP domain consensus sequence [N-X7-R/K-X9-L-X6-L-X6-L] are shown at the top of the picture. Vertical bars with different colors on the left show different subfamilies. The black and gray shades in the picture present the same and similar amino acids, respectively. (XLSX 23 kb)
DOI: 10.6084/m9.figshare.8045888
title: Additional file 5: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S4. Cis-elements associated with abiotic stress in promoter region of ItfbZIPs. (XLS 38 kb)
DOI: 10.6084/m9.figshare.8045912
title: Additional file 7: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S6. Expression pattern of ItfbZIPs under abiotic stresses. (XLSX 38 kb)
DOI: 10.6084/m9.figshare.19580351.v2
title: Transcriptome analysis of adipocytokines and their-related LncRNAs in lung adenocarcinoma revealing the association with prognosis, immune infiltration, and metabolic characteristics

description: Lung adenocarcinoma (LUAD) is amongst the major contributors to cancer-related deaths on a global scale. Adipocytokines and long non-coding RNAs (lncRNAs) are indispensable participants in cancer. We performed a pan-cancer analysis of the mRNA expression, single nucleotide variation, copy number variation, and prognostic value of adipocytokines. LUAD samples were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Simultaneously, train, internal and external cohorts were grouped. After a stepwise screening of optimized genes through least absolute shrinkage and selection operator regression analysis, random forest algorithm,, and Cox regression analysis, an adipocytokine-related prognostic signature (ARPS) with superior performance compared with four additional well-established signatures for survival prediction was constructed. After determination of risk levels, the discrepancy of immune microenvironment, immune checkpoint gene expression, immune subtypes, and immune response in low- and high-risk cohorts were explored through multiple bioinformatics methods. Abnormal pathways underlying high- and low-risk subgroups were identified through gene set enrichment analysis (GSEA). Immune-and metabolism-related pathways that were correlated with risk score were selected through single sample GSEA. Finally, a nomogram with satisfied predictive survival probability was plotted. In summary, this study offers meaningful information for clinical treatment and scientific investigation.
DOI: 10.6084/m9.figshare.19580351.v1
title: Transcriptome Analysis of Adipocytokines and Their-related LncRNAs in Lung Adenocarcinoma Revealing the Association with Prognosis, Immune Infiltration, and Metabolic Characteristics

description: Lung adenocarcinoma (LUAD) is amongst the major contributors to cancer-related deaths on a global scale. Adipocytokines have an impact on immune and metabolism. Long non-coding RNAs (lncRNAs) are indispensable participants in cancer. We performed a pan-cancer analysis of the mRNA expression, single nucleotide variation, copy number variation, and prognostic value of adipocytokines, and displayed the results in heat maps. LUAD samples were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Simultaneously, train, internal and external cohorts were grouped. After a stepwise screening of optimized genes through least absolute shrinkage and selection operator regression analysis, univariate Cox regression analysis, random forest, and multivariate Cox regression analysis, an adipocytokine-related prognostic signature (ARPS) with superior performance compared with four additional well-established signatures for survival prediction was constructed. After determination of risk levels, the discrepancy of immune microenvironment, immune checkpoint gene expression, immune subtypes, and immune response in low- and high-risk cohorts were explored through multiple bioinformatics methods such as ESTIMATE, EPIC, CIBERSORT, XCELL, CIBERSORT-ABS, MCPCOUNTER, QUANTISEQ, and TIMER algorithms. Abnormal pathways underlying high- and low-risk subgroups were identified through gene set enrichment analysis (GSEA). Immune-related pathways together with metabolism-related pathways that were correlated with risk score were selected with the aid of a single sample gene set enrichment analysis (ssGSEA). Finally, a nomogram was plotted with satisfied predictive survival probability which was verified by calibration curves. In summary, this study offers meaningful information that will be used to assist and guide clinical treatment and scientific investigation.
DOI: 10.6084/m9.figshare.8045849.v1
title: Additional file 2: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S2. Distribution of bZIP transcription factors in eukaryotes. (XLSX 11 kb)
DOI: 10.6084/m9.figshare.8045861
title: Additional file 3: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S3. Accession numbers of bZIP genes in Ipomoea trifida, Arabidopsis thaliana and Solanum lycopersicum. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.8045918
title: Additional file 8: of Genome-wide identification, structural and gene expression analysis of the bZIP transcription factor family in sweet potato wild relative Ipomoea trifida

description: Table S7. Primers of the ItfbZIP genes and housekeeping gene for qRT-PCR. (XLSX 10 kb)
DOI: 10.6084/m9.figshare.19580351
title: Transcriptome analysis of adipocytokines and their-related LncRNAs in lung adenocarcinoma revealing the association with prognosis, immune infiltration, and metabolic characteristics

description: Lung adenocarcinoma (LUAD) is amongst the major contributors to cancer-related deaths on a global scale. Adipocytokines and long non-coding RNAs (lncRNAs) are indispensable participants in cancer. We performed a pan-cancer analysis of the mRNA expression, single nucleotide variation, copy number variation, and prognostic value of adipocytokines. LUAD samples were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Simultaneously, train, internal and external cohorts were grouped. After a stepwise screening of optimized genes through least absolute shrinkage and selection operator regression analysis, random forest algorithm,, and Cox regression analysis, an adipocytokine-related prognostic signature (ARPS) with superior performance compared with four additional well-established signatures for survival prediction was constructed. After determination of risk levels, the discrepancy of immune microenvironment, immune checkpoint gene expression, immune subtypes, and immune response in low- and high-risk cohorts were explored through multiple bioinformatics methods. Abnormal pathways underlying high- and low-risk subgroups were identified through gene set enrichment analysis (GSEA). Immune-and metabolism-related pathways that were correlated with risk score were selected through single sample GSEA. Finally, a nomogram with satisfied predictive survival probability was plotted. In summary, this study offers meaningful information for clinical treatment and scientific investigation.
DOI: 10.6084/m9.figshare.10041164
title: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

description: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
DOI: 10.6084/m9.figshare.10041164.v1
title: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

description: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
DOI: 10.6084/m9.figshare.10041167
title: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

description: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa
DOI: 10.6084/m9.figshare.10041167.v1
title: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa

description: of Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa