cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.21834266
title: Optimal linear discriminant analysis for high-dimensional functional data

description: Most of existing methods of functional data classification deal with one or a few processes. In this work we tackle classification of high-dimensional functional data, in which each observation is potentially associated with a large number of functional processes, p, which is comparable to or even much larger than the sample size n. The challenge arises from the complex inter-correlation structures among multiple functional processes, instead of a diagonal correlation for a single process. Since truncation is often needed for approximation in functional data, another difficulty stems from the fact that the discriminant set of the infinite-dimensional optimal classifier may be different from that of the truncated optimal classifier, when multiple (especially a large number of) processes are involved. We bridge the gap by proposing a penalized classifier that achieves both near-perfect classification that is unique to functional data, and discriminant set inclusion consistency in the sense that the classification-responsible functional predictors includes those of the underlying optimal classifier. Simulation study and real data application are carried out to demonstrate its favorable performance.
DOI: 10.6084/m9.figshare.16590996.v1
title: Additional file 3 of ALKBH5-HOXA10 loop-mediated JAK2 m6A demethylation and cisplatin resistance in epithelial ovarian cancer

description: Additional file 3 The differentially expressed genes of mRNA-seq (|log2 (FC)| ≥ 1, p &lt;0.05).
DOI: 10.6084/m9.figshare.21835258.v1
title: The impact of agricultural comprehensive development on agro-ecological efficiency of China - evidence from perspective of scale and structure

description: ABSTRACT: Promoting the agricultural sustainable development is one of the core objectives of agricultural comprehensive development (ACD), and the core of agricultural sustainable development lies in enhancing agro-ecological efficiency (AEE). Based on inter-provincial panel data from 2003-2017, the AEE was measured by a unexpected super-efficient SBM model. From the perspective of investment scale and investment structure, the impact of investment scale in ACD on AEE was examined using a panel econometric model, then characterizing the investment structure by the proportion of government funds in the investment of ACD, examining the non-linear relationship between investment structure of ACD and AEE seeking a reasonable proportion of government expenditure. Finally, a spatial econometric model was constructed to test the spatial spillover effect of the scale and structure of investment in ACD on AEE. Results showed that: (i) AEE of China is on the rise overall, but the efficiency level is still low and there is large scope for improvement. (ii) Due to the inefficient use of funds and the lag in the transformation of agricultural benefits, the scale of investment in ACD has a significant negative impact on AEE in the current period. (iii) The impact of investment structure of ACD on AEE presents a significant “inverted N” relationship, and the optimal proportion of government fund investment structure is 76.71%. The reasonable structure of investment in ACD at different food functional areas shows differences. (iv) After considering the spatial effect, the impact of ACD remains robust, but the spatial spillover effect prolongs the time lag of this impact of investment scale and starts to have a positive impact in the 2nd year after the investment. Guarantee the investment scale in ACD, reduce financial redundancy, establish a cooperation mechanism between ACD and agricultural ecological protection in neighboring areas, and increase the introduction of private capital can achieve sustainable development of agricultural economy.
DOI: 10.5281/zenodo.10678879
title: Dataset for "Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses"

description: Dataset for "Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses"
DOI: 10.5281/zenodo.10678880
title: Dataset for "Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses"

description: Dataset for "Transient grating spectroscopy on a DyCo5 thin film with femtosecond extreme ultraviolet pulses"
DOI: 10.6084/m9.figshare.11872506
title: Independent origins of diploidy in <i>Metarhizium</i>

description: In fungi, stable diploid genome arrangements are rare. Here we present evidence from nuclear intergenic DNA sequencing, microsatellite genotyping, and configuration of the mating-type locus to demonstrate two independent origins of persistent diploid genome organization in the <i>Metarhizium majus</i> species complex. Most taxa in the complex are genotypically haploid, with individual isolates consistently displaying a single allele across all nuclear loci, as well as having a single mating-type locus. In contrast, individuals of <i>M. majus</i> and the clade designated here MGT1 are shown to be diploid, based on a consistent finding of heterozygosity and the presence of both <i>MAT1</i> and <i>MAT2</i> mating-type loci. In single locus phylogenies, nuclear intergenic alleles of <i>M. majus</i> and MGT1 each form monophyletic groups, indicating that diploidy in both taxa likely originated by the union of conspecific individuals. Sequence divergence in the <i>APN2/MAT1-1-3</i> and <i>APN2/MAT2-1</i> intergenic spacers indicate the two MAT loci are physically separated in the genomes of both diploid taxa, although the linkage relationship of the MAT loci to one another is unknown. The presence of both mating genes in a single nucleus suggests these diploid genomes may represent a mating event that failed to complete meiosis. Whether or not these isolates are able to complete the sexual cycle under any conditions and form ascospores remains an open question.
DOI: 10.6084/m9.figshare.11872506.v1
title: Independent origins of diploidy in <i>Metarhizium</i>

description: In fungi, stable diploid genome arrangements are rare. Here we present evidence from nuclear intergenic DNA sequencing, microsatellite genotyping, and configuration of the mating-type locus to demonstrate two independent origins of persistent diploid genome organization in the <i>Metarhizium majus</i> species complex. Most taxa in the complex are genotypically haploid, with individual isolates consistently displaying a single allele across all nuclear loci, as well as having a single mating-type locus. In contrast, individuals of <i>M. majus</i> and the clade designated here MGT1 are shown to be diploid, based on a consistent finding of heterozygosity and the presence of both <i>MAT1</i> and <i>MAT2</i> mating-type loci. In single locus phylogenies, nuclear intergenic alleles of <i>M. majus</i> and MGT1 each form monophyletic groups, indicating that diploidy in both taxa likely originated by the union of conspecific individuals. Sequence divergence in the <i>APN2/MAT1-1-3</i> and <i>APN2/MAT2-1</i> intergenic spacers indicate the two MAT loci are physically separated in the genomes of both diploid taxa, although the linkage relationship of the MAT loci to one another is unknown. The presence of both mating genes in a single nucleus suggests these diploid genomes may represent a mating event that failed to complete meiosis. Whether or not these isolates are able to complete the sexual cycle under any conditions and form ascospores remains an open question.
DOI: 10.6084/m9.figshare.14494575
title: MicroRNA-140-3p alleviates intervertebral disc degeneration <i>via</i> KLF5/N-cadherin/MDM2/Slug axis

description: MicroRNAs (miRNAs) are associated with healing or deteriorating degenerated intervertebral disc (IVD) tissues in spinal cord diseases, including intervertebral disc degeneration (IDD). IDD represents a chronic process of extracellular matrix destruction, but the relevant molecular mechanisms implicated in the regenerative effects of miRNAs are unclear. Here, we investigated the regenerative effects of microRNA-140 (miR-140-3p) in an IDD model induced by annulus needle puncture. Bioinformatics analysis was conducted to identify regulatory factors (KLF5/N-cadherin/MDM2/Slug) linked to miR-140-3p effects in IDD. Mesenchymal stem cells (MSCs) were extracted from degenerated IVD nucleus pulposus (NP), and the expression of miR-140-3p/KLF5/N-cadherin/MDM2/Slug was manipulated to explore their effects on cell proliferation, migration, apoptosis and differentiation. The results showed that miR-140-3p was under-expressed in the degenerated IVD NP, whereas its overexpression alleviated IDD. Mechanistic studies suggested that miR-140-3p targeted KLF5 expression, and high KLF5 expression impeded the migration and differentiation of MSCs. In degenerated IVD NP-derived MSCs, MiR-140-3p-mediated KLF5 downregulation simultaneously elevated N-cadherin expression and transcriptionally inhibited MDM2, thus upregulating Slug expression. The experimental data indicated that miR-140-3p enhanced the proliferation, migration and differentiation of degenerated IVD NP-derived MSCs and repressed their apoptosis. The <i>in vivo</i> validation experiment also demonstrated that miR-140-3p inhibited IDD by modulating the KLF5/N-cadherin/MDM2/Slug axis. Collectively, our results uncovered the regenerative role of miR-140-3p in IDD via regulation of the KLF5/N-cadherin/MDM2/Slug axis, which could be a potential therapeutic target for IDD. <b>Abbreviations:</b> miR-140-3p: microRNA-140-3p; IDD: intervertebral disc degeneration; MSCs: Mesenchymal stem cells; IVD: intervertebral disc; MSCs: mesenchymal stem cells; KLF5: Kruppel-like factor 5; MDM2: mouse double minute 2; NC: negative control; DHI: disc height index
DOI: 10.6084/m9.figshare.20261326.v1
title: <i>ACPY2</i> gene polymorphisms on cancer risk: a systematic review and meta-analysis

description: To provide a comprehensive account of the association of <i>ACYP2</i> gene polymorphisms with susceptibility to cancer. A literature search for eligible candidate gene studies published before April 20, 2022 was conducted in the PubMed, Medline and Web of Science. The following combinations of main keywords were used: (ACYP2 OR acylphosphatase 2) AND (polymorphism OR mutation OR variation OR SNP OR genotype) AND (cancer OR tumor OR neoplasm OR malignancy OR carcinoma OR adenocarcinoma). Potential sources of heterogeneity were sought out via subgroup and sensitivity analysis. Publication bias were also estimated. Overall, a total of 10 articles with 5,230 cases and 5,086 controls for thirteen polymorphisms of <i>ACYP2</i> gene were enrolled. We found that <i>ACYP2</i> rs11125529, rs11896604, rs12615793, rs17045754, rs6713088, rs843645, rs843706, rs843711 and rs843752 were correlated with an increased risk of cancer. However, we found that <i>ACYP2</i> rs12621038 might have less susceptibility to cancer. While for other polymorphisms, the results showed no significant association with cancer risk. <i>ACYP2</i> rs11125529, rs11896604, rs12615793, rs17045754, rs6713088, rs843645, rs843706, rs843711 and rs843752 are associated with cancer risk. <i>ACYP2</i> rs12621038 polymorphism is inversely associated with cancer risk.
DOI: 10.6084/m9.figshare.21834260
title: Compositional Graphical Lasso Resolves the Impact of Parasitic Infection on Gut Microbial Interaction Networks in a Zebrafish Model

description: Understanding how microbes interact with each other is key to revealing the underlying role that microorganisms play in the host or environment and to identifying microorganisms as an agent that can potentially alter the host or environment. For example, understanding how the microbial interactions associate with parasitic infection can help resolve potential drug or diagnostic test for parasitic infection. To unravel the microbial interactions, existing tools often rely on graphical models to infer the conditional dependence of microbial abundances to represent their interactions. However, current methods do not simultaneously account for the discreteness, compositionality, and heterogeneity inherent to microbiome data. Thus, we build a new approach called “compositional graphical lasso” upon existing tools by incorporating the above characteristics into the graphical model explicitly. We illustrate the advantage of compositional graphical lasso over current methods under a variety of simulation scenarios and on a benchmark study, the Tara Oceans Project. Moreover, we present our results from the analysis of a dataset from the Zebrafish Parasite Infection Study, which aims to gain insight into how the gut microbiome and parasite burden covary during infection, thus uncovering novel putative methods of disrupting parasite success. Our approach identifies changes in interaction degree between infected and uninfected individuals for three taxa, Photobacterium, Gemmobacter, and Paucibacter, which are inversely predicted by other methods. Further investigation of these method-specific taxa interaction changes reveals their biological plausibility. In particular, we speculate on the potential pathobiotic roles of Photobacterium and Gemmobacter in the zebrafish gut, and the potential probiotic role of Paucibacter. Collectively, our analyses demonstrate that compositional graphical lasso provides a powerful means of accurately resolving interactions between microbiota and can thus drive novel biological discovery.
DOI: 10.6084/m9.figshare.16590839
title: Additional file 8 of RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources

description: Additional file 8. Folder S4: RPDescriptor program code for shape classification of RNA pockets.
DOI: 10.6084/m9.figshare.7679516
title: Additional file 3: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S2. List of differentially expressed genes with more than 4-fold change between any two samples (XLSX 1204 kb)
DOI: 10.6084/m9.figshare.20261326
title: <i>ACPY2</i> gene polymorphisms on cancer risk: a systematic review and meta-analysis

description: To provide a comprehensive account of the association of <i>ACYP2</i> gene polymorphisms with susceptibility to cancer. A literature search for eligible candidate gene studies published before April 20, 2022 was conducted in the PubMed, Medline and Web of Science. The following combinations of main keywords were used: (ACYP2 OR acylphosphatase 2) AND (polymorphism OR mutation OR variation OR SNP OR genotype) AND (cancer OR tumor OR neoplasm OR malignancy OR carcinoma OR adenocarcinoma). Potential sources of heterogeneity were sought out via subgroup and sensitivity analysis. Publication bias were also estimated. Overall, a total of 10 articles with 5,230 cases and 5,086 controls for thirteen polymorphisms of <i>ACYP2</i> gene were enrolled. We found that <i>ACYP2</i> rs11125529, rs11896604, rs12615793, rs17045754, rs6713088, rs843645, rs843706, rs843711 and rs843752 were correlated with an increased risk of cancer. However, we found that <i>ACYP2</i> rs12621038 might have less susceptibility to cancer. While for other polymorphisms, the results showed no significant association with cancer risk. <i>ACYP2</i> rs11125529, rs11896604, rs12615793, rs17045754, rs6713088, rs843645, rs843706, rs843711 and rs843752 are associated with cancer risk. <i>ACYP2</i> rs12621038 polymorphism is inversely associated with cancer risk.
DOI: 10.6084/m9.figshare.7679516.v1
title: Additional file 3: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S2. List of differentially expressed genes with more than 4-fold change between any two samples (XLSX 1204 kb)
DOI: 10.6084/m9.figshare.7679522.v1
title: Additional file 5: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S4. List of DEGs up-regulated in pad4â 1 sid2â 1 (XLSX 98 kb)
DOI: 10.6084/m9.figshare.7679528
title: Additional file 7: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S8. List of Cysteine-rich receptor-like protein kinases differentially expressed in Col-0 and pad4â 1 sid2â 1 (XLSX 25 kb)
DOI: 10.6084/m9.figshare.21311021.v1
title: Additional file 5 of STAT3/miR-130b-3p/MBNL1 feedback loop regulated by mTORC1 signaling promotes angiogenesis and tumor growth

description: Additional file 5: Supplementary Table 9. List of the downregulated differentially expressed genes from DEGs in angiofibroma(AF) of TSC patients vs. normal skin. All genes were identified with FDR-adjusted p-value &lt; 0.05 and absolute value of log2(FC) &gt; 1.
DOI: 10.6084/m9.figshare.21311028
title: Additional file 3 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

description: Additional file 3: Table S1 Analysis of variance for LL, LW and LA in an F1 population using mixed model for two years in two locations (CP and LF)
DOI: 10.6084/m9.figshare.21311028.v1
title: Additional file 3 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

description: Additional file 3: Table S1 Analysis of variance for LL, LW and LA in an F1 population using mixed model for two years in two locations (CP and LF)
DOI: 10.6084/m9.figshare.21311031.v1
title: Additional file 4 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

description: Additional file 4: Table S2. List of 2,443 leaf-specific genes.
DOI: 10.6084/m9.figshare.21311034
title: Additional file 5 of Combining QTL mapping and RNA-Seq Unravels candidate genes for Alfalfa (Medicago sativa L.) leaf development

description: Additional file 5: Table S3. List of 2,061 up-regulated genes (‘sativa’ Vs ‘falcata’).
DOI: 10.6084/m9.figshare.7679489
title: Additional file 10: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S10. Primers for qRT-PCR in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.7679489.v1
title: Additional file 10: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S10. Primers for qRT-PCR in this study (XLSX 10 kb)
DOI: 10.6084/m9.figshare.11873862.v2
title: Extreme and Inference for Tail Gini Functionals With Applications in Tail Risk Measurement

description: Tail risk analysis focuses on the problem of risk measurement on the tail regions of financial variables. As one crucial task in tail risk analysis for risk management, the measurement of tail risk variability is less addressed in the literature. Neither the theoretical results nor inference methods are fully developed, which results in the difficulty of modeling implementation. Practitioners are then short of measurement methods to understand and evaluate tail risks, even when they have large amounts of valuable data in hand. In this article, we consider the measurement of tail variability under the tail scenarios of a systemic variable by extending the Gini’s methodology. As we are very interested in the limit of the proposed measures as the risk level approaches to the extreme status, we showed, by using extreme value techniques, how the tail dependence structure and marginal risk severity have influences on the limit of the proposed tail variability measures. We construct a nonparametric estimator, and its asymptotic behavior is explored. Furthermore, to provide practitioners with more measures for tail risk, we construct three coefficients/measures for tail risks from different views toward tail risks and illustrate them in a real data analysis. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7679519
title: Additional file 4: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S3. List of DEGs up-regulated in Col-0 (XLSX 164 kb)
DOI: 10.6084/m9.figshare.7679528.v1
title: Additional file 7: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S8. List of Cysteine-rich receptor-like protein kinases differentially expressed in Col-0 and pad4â 1 sid2â 1 (XLSX 25 kb)
DOI: 10.6084/m9.figshare.7679531.v1
title: Additional file 8: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

description: Table S9. List of differentially expressed UGT genes in pad4â 1 sid2â 1 and Col-0 (XLSX 23 kb)
DOI: 10.6084/m9.figshare.14494575.v1
title: MicroRNA-140-3p alleviates intervertebral disc degeneration <i>via</i> KLF5/N-cadherin/MDM2/Slug axis

description: MicroRNAs (miRNAs) are associated with healing or deteriorating degenerated intervertebral disc (IVD) tissues in spinal cord diseases, including intervertebral disc degeneration (IDD). IDD represents a chronic process of extracellular matrix destruction, but the relevant molecular mechanisms implicated in the regenerative effects of miRNAs are unclear. Here, we investigated the regenerative effects of microRNA-140 (miR-140-3p) in an IDD model induced by annulus needle puncture. Bioinformatics analysis was conducted to identify regulatory factors (KLF5/N-cadherin/MDM2/Slug) linked to miR-140-3p effects in IDD. Mesenchymal stem cells (MSCs) were extracted from degenerated IVD nucleus pulposus (NP), and the expression of miR-140-3p/KLF5/N-cadherin/MDM2/Slug was manipulated to explore their effects on cell proliferation, migration, apoptosis and differentiation. The results showed that miR-140-3p was under-expressed in the degenerated IVD NP, whereas its overexpression alleviated IDD. Mechanistic studies suggested that miR-140-3p targeted KLF5 expression, and high KLF5 expression impeded the migration and differentiation of MSCs. In degenerated IVD NP-derived MSCs, MiR-140-3p-mediated KLF5 downregulation simultaneously elevated N-cadherin expression and transcriptionally inhibited MDM2, thus upregulating Slug expression. The experimental data indicated that miR-140-3p enhanced the proliferation, migration and differentiation of degenerated IVD NP-derived MSCs and repressed their apoptosis. The <i>in vivo</i> validation experiment also demonstrated that miR-140-3p inhibited IDD by modulating the KLF5/N-cadherin/MDM2/Slug axis. Collectively, our results uncovered the regenerative role of miR-140-3p in IDD via regulation of the KLF5/N-cadherin/MDM2/Slug axis, which could be a potential therapeutic target for IDD. <b>Abbreviations:</b> miR-140-3p: microRNA-140-3p; IDD: intervertebral disc degeneration; MSCs: Mesenchymal stem cells; IVD: intervertebral disc; MSCs: mesenchymal stem cells; KLF5: Kruppel-like factor 5; MDM2: mouse double minute 2; NC: negative control; DHI: disc height index