cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12774951
title: Additional file 6 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation

description: Additional file 6: Table S5. RIP-seq analysis of 293 T cells transfected with SERBP1-streptag. Sheet 1, summary of results; sheet 2, list of SERBP1 target genes; sheet 3, gene ontology analysis; sheet 4, metabolism terms enriched in the GO analysis; sheet 5, Panther pathways analysis; sheet 6, KEGG pathway analysis.
DOI: 10.6084/m9.figshare.12774951.v1
title: Additional file 6 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation

description: Additional file 6: Table S5. RIP-seq analysis of 293 T cells transfected with SERBP1-streptag. Sheet 1, summary of results; sheet 2, list of SERBP1 target genes; sheet 3, gene ontology analysis; sheet 4, metabolism terms enriched in the GO analysis; sheet 5, Panther pathways analysis; sheet 6, KEGG pathway analysis.
DOI: 10.6084/m9.figshare.12774960.v1
title: Additional file 9 of The RNA-binding protein SERBP1 functions as a novel oncogenic factor in glioblastoma by bridging cancer metabolism and epigenetic regulation

description: Additional file 9: Table S8. Gene expression correlation analysis. Genes showing positive and negative (anti-correlation) with SERBP1 in TCGA GBM samples according to R2. Sheet 1, genes showing positive correlation with SERBP1 in TCGA GBM samples; sheet 2, GO analysis of genes showing positive correlation with SERBP1 in TCGA GBM samples; sheet 3, genes showing anti-correlation with SERBP1 in TCGA GBM samples; sheet 4, GO analysis of genes showing anti-correlation with SERBP1 in TCGA GBM samples; sheet 5, comparison between enriched GO terms in genes negatively correlated with SERBP1 vs. genes upregulated upon SERBP1 knockdown.
DOI: 10.6084/m9.figshare.18542244.v1
title: Identification of prognostic biomarkers in papillary renal cell carcinoma and PTTG1 may serve as a biomarker for predicting immunotherapy response

description: This study aims to identify potential prognostic and therapeutic biomarkers in papillary renal cell carcinoma (pRCC). Two microarray datasets were downloaded from the Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified. The protein-protein interaction (PPI) networks and functional annotations of DEGs were established. Survival analysis was utilized to evaluate the prognostic significance of the DEGs and the association between the expression level of candidate biomarkers and various tumour-infiltrating immune cells was explored. The role of <i>PTTG1</i> in tumour microenvironments (TME) was further explored using Single-cell RNA-seq and its prognostic and therapeutic significance was validated in Fudan University Shanghai Cancer Centre (FUSCC) cohort. Eight genes, including <i>BUB1B</i>, <i>CCNB1</i>, <i>CCNB2</i>, <i>MAD2L1</i>, <i>TTK</i>, <i>CDC20</i>, <i>PTTG1,</i> and <i>MCM</i> were found to be negatively associated with patients’ prognosis. The expression level of <i>PTTG1</i> was found to be significantly associated with lymphocytes, immunomodulators, and chemokine in the TCGA cohort. Single-cell RNA-seq information indicated that <i>PTTG1</i> was strongly associated with the proliferation of T cells. In the FUSCC cohort, the expression level of PTTG1 was also statistically significant for both progression-free survival (PFS) and overall survival (OS) prediction (HR = 2.683, <i>p</i> &lt; .001; HR = 2.673, <i>p</i> = .001). And higher expression level of PTTG1 was significantly associated with immune checkpoint blockade (ICB) response in the FUSCC cohort (<i>χ</i><sup>2</sup>=3.99, <i>p</i><b> </b>&lt;<b> </b>.05). Eight genes were identified as a prognostic biomarker and the expression level of PTTG1 was also found to serve as a potential predictor for ICB response in pRCC patients.Key messages:Eight genes, including <i>BUB1B</i>, <i>CCNB1</i>, <i>CCNB2</i>, <i>MAD2L1</i>, <i>TTK</i>, <i>CDC20</i>, <i>PTTG1,</i> and <i>MCM</i> were found to be negatively associated with pRCC patients’ prognosis.Expression level of PTTG1 was significantly associated with tumour microenvironment including lymphocytes, immunomodulators, and chemokines.Higher expression level of PTTG1 was significantly associated with immune checkpoint blockade (ICB) response in FUSCC cohort Eight genes, including <i>BUB1B</i>, <i>CCNB1</i>, <i>CCNB2</i>, <i>MAD2L1</i>, <i>TTK</i>, <i>CDC20</i>, <i>PTTG1,</i> and <i>MCM</i> were found to be negatively associated with pRCC patients’ prognosis. Expression level of PTTG1 was significantly associated with tumour microenvironment including lymphocytes, immunomodulators, and chemokines. Higher expression level of PTTG1 was significantly associated with immune checkpoint blockade (ICB) response in FUSCC cohort
DOI: 10.6084/m9.figshare.9105032.v3
title: Empirical Likelihood Ratio Tests of Conditional Moment Restrictions With Unknown Functions

description: This article introduces empirical likelihood ratio tests for conditional moment models in which the unknown parameter contains infinite-dimensional components. We allow unknown functions to be included in the conditional moment restrictions. We discusses (1) the limiting distribution of the sieve conditional empirical likelihood ratio (SCELR) test statistic for functionals of parameters under the null hypothesis and local alternatives; and (2) the limiting distribution of the SCELR test statistic for conditional moment restrictions (a consistent specification test) under the null hypothesis and local alternatives. A Monte Carlo study examines finite sample performance. We then apply these tests in an empirical application to construct confidence intervals for Engel curves and test restrictions on the curves.
DOI: 10.6084/m9.figshare.12775195
title: Additional file 3 of Using full chloroplast genomes of ‘red’ and ‘yellow’ Bixa orellana (achiote) for kmer based identification and phylogenetic inference

description: Additional file 3: Table S3. Phylip formatted D2 distance matrix from kmer distances.
DOI: 10.6084/m9.figshare.7532234
title: Additional file 4: of MLH1 enhances the sensitivity of human endometrial carcinoma cells to cisplatin by activating the MLH1/c-Abl apoptosis signaling pathway

description: Table S1. The information about the sequences. (XLS 21 kb)
DOI: 10.6084/m9.figshare.12775189.v1
title: Additional file 1 of Using full chloroplast genomes of ‘red’ and ‘yellow’ Bixa orellana (achiote) for kmer based identification and phylogenetic inference

description: Additional file 1: Table S1. Accession numbers, Family, Genus and species of all chloroplasts used for phylogenetic analyses.
DOI: 10.6084/m9.figshare.12775003
title: Additional file 1 of Physiological change alters endophytic bacterial community in clubroot of tumorous stem mustard infected by Plasmodiophora brassicae

description: Additional file 1: Table S1. Taxonomy and distribution of the OTUs. Taxonomy at phylum, class, order, family, genus, species and OTU level. R, healthy roots. C, clubroots. The numbers in table cells are numbers of sequences of each OTU.
DOI: 10.6084/m9.figshare.13290707
title: Additional file 11 of DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies

description: Additional file 11: Table S9. Results of enrichment analyses for CpGs associated with BMI in previously reported large EWAS (N≥1000).
DOI: 10.6084/m9.figshare.13290707.v1
title: Additional file 11 of DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies

description: Additional file 11: Table S9. Results of enrichment analyses for CpGs associated with BMI in previously reported large EWAS (N≥1000).
DOI: 10.6084/m9.figshare.13290713.v1
title: Additional file 12 of DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies

description: Additional file 12: Table S10. Results of functional enrichment analyses using genes linked to the CpGs with p-values &lt; 1-x10-4 in each of the models using Gene Ontology (GO) terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) terms (FDR &lt;0.05).
DOI: 10.6084/m9.figshare.12775239.v1
title: Additional file 8 of Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

description: Additional file 8: Table S3. Genes for qRT-PCR.
DOI: 10.6084/m9.figshare.12775242.v1
title: Additional file 9 of Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

description: Additional file 9: Appendix S1. primers in this study.
DOI: 10.6084/m9.figshare.12775282.v1
title: Additional file 1 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 1.
DOI: 10.6084/m9.figshare.16969301.v1
title: Additional file 5 of Durations of asymptomatic, symptomatic, and care-seeking phases of tuberculosis disease with a Bayesian analysis of prevalence survey and notification data

description: Additional file 5. Extracted data, Kenya. TB prevalence data were from Enos et al.
DOI: 10.6084/m9.figshare.12775236.v1
title: Additional file 7 of Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

description: Additional file 7: Table S2. genes were significantly differentially expressed in Y12–4.
DOI: 10.6084/m9.figshare.12775291
title: Additional file 4 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 4.
DOI: 10.6084/m9.figshare.16969292
title: Additional file 2 of Durations of asymptomatic, symptomatic, and care-seeking phases of tuberculosis disease with a Bayesian analysis of prevalence survey and notification data

description: Additional file 2. TB prevalence survey characteristics
DOI: 10.6084/m9.figshare.12775294.v1
title: Additional file 5 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 5.
DOI: 10.6084/m9.figshare.16960660.v1
title: Additional file 2 of TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

description: Additional file 2: Supplementary Table 1. The genomic coordinates of chromatin tracing target regions on human X chromosome.
DOI: 10.6084/m9.figshare.12775285
title: Additional file 2 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 2.
DOI: 10.6084/m9.figshare.16969298.v1
title: Additional file 4 of Durations of asymptomatic, symptomatic, and care-seeking phases of tuberculosis disease with a Bayesian analysis of prevalence survey and notification data

description: Additional file 4. Extracted data, Blantyre Malawi
DOI: 10.6084/m9.figshare.16969295.v1
title: Additional file 3 of Durations of asymptomatic, symptomatic, and care-seeking phases of tuberculosis disease with a Bayesian analysis of prevalence survey and notification data

description: Additional file 3. Extracted data, 11 included settings
DOI: 10.6084/m9.figshare.12775288
title: Additional file 3 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 3.
DOI: 10.6084/m9.figshare.12775294
title: Additional file 5 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 5.
DOI: 10.6084/m9.figshare.12775297
title: Additional file 6 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 6.
DOI: 10.6084/m9.figshare.12775300
title: Additional file 7 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 7.
DOI: 10.6084/m9.figshare.12775300.v1
title: Additional file 7 of Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation

description: Additional file 7.
DOI: 10.6084/m9.figshare.16969298
title: Additional file 4 of Durations of asymptomatic, symptomatic, and care-seeking phases of tuberculosis disease with a Bayesian analysis of prevalence survey and notification data

description: Additional file 4. Extracted data, Blantyre Malawi
DOI: 10.6084/m9.figshare.24533320.v1
title: Role and potential of the semi-classical/-quantum mechanism of the extracellular environment and cell envelope in Direct Interspecies Electron Transfer (DIET)-driven biomethanation

description: The extracellular electron transfer (EET) capability of <i>Methanosarcina</i> spp. in direct interspecies electron transfer (DIET) has profoundly increased our understanding of microbial kinetics and energetics in biomethanation systems. In <i>Methanosarcina</i> spp., such EET mechanisms occur in the cell envelope and biofilm matrix. These substances are composed of protein-like, polysaccharide-rich biomolecular structures that were previously thought to contribute only to cell support and shape; while their participation in dynamic processes remains unclear and has gathered widespread interest. This review first addresses the molecular structure and chemical characteristics of the extracellular matrix and cell wall polymers in <i>Methanosarcina</i> spp. Next, we focus on recent theoretical studies on the conduction and EET mechanisms of the extracellular matrix and cell wall polymers: tunnelling, hopping, proton-activated electron transfer and voltage-dependent electron transport. We conclude this review by discussing the state-of-the-art electrochemical techniques and experiments and the associated challenges, i.e., the kinetic isotope effect and on–off resonance switching. The border impacts of such conductive pathways may offer a semi-classical/quantum perspective on microbiology and mark the renaissance of anaerobic biotechnology.
DOI: 10.6084/m9.figshare.24187491
title: Potential sources and occurrence of macro-plastics and microplastics pollution in farmland soils: A typical case of China

description: Plastic debris (including macro-plastics, microplastics (MPs), and nanoplastics), defined as an emerging contaminant, has been proven to significantly affect soil ecosystem functioning. Accordingly, there is an urgent need to robustly quantify the pollution situation and potential sources of plastics in soils. China as the leading producer and user of agricultural plastics is analyzed as a typical case study to highlight the current situation of farmland macro-plastics and MPs. Our study summarized information on the occurrence and abundance of macro-plastics and MPs in Chinese farmland soils for the first time based on 163 publications with 728 sample sites. The results showed that the average concentration of macro-plastics, and the abundance of MPs in Chinese farmlands were 103 kg ha<sup>−1</sup> and 4537 items kg<sup>−1</sup> (dry soil), respectively. In addition, this study synthesized the latest scientific evidence on sources of macro-plastics and MPs in farmland soils. Agricultural plastic films and organic wastes are the most reported sources, indicating that they contribute significantly to plastic debris in agricultural soils. Furthermore, the modeling methods for quantifying macro-plastics and MPs in soils and estimating the stock and flow of plastic materials within agricultural systems were also summarized.
DOI: 10.6084/m9.figshare.24187491.v1
title: Potential sources and occurrence of macro-plastics and microplastics pollution in farmland soils: A typical case of China

description: Plastic debris (including macro-plastics, microplastics (MPs), and nanoplastics), defined as an emerging contaminant, has been proven to significantly affect soil ecosystem functioning. Accordingly, there is an urgent need to robustly quantify the pollution situation and potential sources of plastics in soils. China as the leading producer and user of agricultural plastics is analyzed as a typical case study to highlight the current situation of farmland macro-plastics and MPs. Our study summarized information on the occurrence and abundance of macro-plastics and MPs in Chinese farmland soils for the first time based on 163 publications with 728 sample sites. The results showed that the average concentration of macro-plastics, and the abundance of MPs in Chinese farmlands were 103 kg ha<sup>−1</sup> and 4537 items kg<sup>−1</sup> (dry soil), respectively. In addition, this study synthesized the latest scientific evidence on sources of macro-plastics and MPs in farmland soils. Agricultural plastic films and organic wastes are the most reported sources, indicating that they contribute significantly to plastic debris in agricultural soils. Furthermore, the modeling methods for quantifying macro-plastics and MPs in soils and estimating the stock and flow of plastic materials within agricultural systems were also summarized.
DOI: 10.6084/m9.figshare.24533320
title: Role and potential of the semi-classical/-quantum mechanism of the extracellular environment and cell envelope in Direct Interspecies Electron Transfer (DIET)-driven biomethanation

description: The extracellular electron transfer (EET) capability of <i>Methanosarcina</i> spp. in direct interspecies electron transfer (DIET) has profoundly increased our understanding of microbial kinetics and energetics in biomethanation systems. In <i>Methanosarcina</i> spp., such EET mechanisms occur in the cell envelope and biofilm matrix. These substances are composed of protein-like, polysaccharide-rich biomolecular structures that were previously thought to contribute only to cell support and shape; while their participation in dynamic processes remains unclear and has gathered widespread interest. This review first addresses the molecular structure and chemical characteristics of the extracellular matrix and cell wall polymers in <i>Methanosarcina</i> spp. Next, we focus on recent theoretical studies on the conduction and EET mechanisms of the extracellular matrix and cell wall polymers: tunnelling, hopping, proton-activated electron transfer and voltage-dependent electron transport. We conclude this review by discussing the state-of-the-art electrochemical techniques and experiments and the associated challenges, i.e., the kinetic isotope effect and on–off resonance switching. The border impacts of such conductive pathways may offer a semi-classical/quantum perspective on microbiology and mark the renaissance of anaerobic biotechnology.
DOI: 10.6084/m9.figshare.13290722.v1
title: Additional file 1 of DNA methylation and body mass index from birth to adolescence: meta-analyses of epigenome-wide association studies

description: Additional file 1: Table S1A-D. Characteristics of the participating studies in the main meta-analyses.
DOI: 10.17028/rd.lboro.23261072
title: Supplementary information files for Microstructure and ionic conductivities of NASICON-type Li₁.₃A1₀.₃Ti₁.₇(PO₄)₃ solid electrolytes produced by cold sintering assisted process

description: Supplementary files for article Microstructure and ionic conductivities of NASICON-type Li₁.₃A1₀.₃Ti₁.₇(PO₄)₃ solid electrolytes produced by cold sintering assisted process
Li1.3Al0.3Ti1.7(PO4)3 (LATP) is a promising solid electrolyte for lithium-ion batteries. However, it is challenging to densify LATP ceramics at reduced sintering temperature while preserving their electrical properties. Herein, LATP ceramics were pre-densified via cold sintering process (CSP) at 250 °C for 1 h and exhibited room temperature ionic conductivity of 2.01 × 10−6 S/cm. Subsequent post-annealing at as low as 900 °C for 1 h resulted in two orders of magnitude improvement in both grain boundary conductivity and total conductivity, compared to those of as-CSPed LATP. The optimal total conductivity (4.29 × 10−4 S/cm) obtained from post-annealed material is among the best reported values so far. It is also 5 times greater than the conductivity (8.51 × 10−5 S/cm) of the conventionally sintered LATP. We propose that post-annealing effectively eliminates amorphous insulating phases generated during CSP and promotes crack-free microstructure with moderate grain growth, which collectively contributes to dramatically enhanced conductivity. This work unambiguously demonstrates that CSP-assisted process can avoid the detrimental effects of high temperature associated with conventional sintering on microstructure and conductivity, and thus is a cost-effective processing route for fabrication of solid-state electrolytes for battery applications. 
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DOI: 10.6084/m9.figshare.16960663
title: Additional file 3 of TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations

description: Additional file 3: Supplementary Table 2. Sequences of the chromatin tracing template oligo pools.