cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19669158
title: Transformation-Invariant Learning of Optimal Individualized Decision Rules with Time-to-Event Outcomes

description: In many important applications of precision medicine, the outcome of interest is time to an event (e.g., death, relapse of disease) and the primary goal is to identify the optimal individualized decision rule (IDR) to prolong survival time. Existing work in this area have been mostly focused on estimating the optimal IDR to maximize the restricted mean survival time in the population. We propose a new robust framework for estimating an optimal static or dynamic IDR with time-to-event outcomes based on an easy-to-interpret quantile criterion. The new method does not need to specify an outcome regression model and is robust for heavy-tailed distribution. The estimation problem corresponds to a nonregular <i>M</i>-estimation problem with both finite and infinite-dimensional nuisance parameters. Employing advanced empirical process techniques, we establish the statistical theory of the estimated parameter indexing the optimal IDR. Furthermore, we prove a novel result that the proposed approach can consistently estimate the optimal value function under mild conditions even when the optimal IDR is nonunique, which happens in the challenging setting of exceptional laws. We also propose a smoothed resampling procedure for inference. The proposed methods are implemented in the R-package QTOCen. We demonstrate the performance of the proposed new methods via extensive Monte Carlo studies and a real data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19669158.v1
title: Transformation-Invariant Learning of Optimal Individualized Decision Rules with Time-to-Event Outcomes

description: In many important applications of precision medicine, the outcome of interest is time to an event (e.g., death, relapse of disease) and the primary goal is to identify the optimal individualized decision rule (IDR) to prolong survival time. Existing work in this area have been mostly focused on estimating the optimal IDR to maximize the restricted mean survival time in the population. We propose a new robust framework for estimating an optimal static or dynamic IDR with time-to-event outcomes based on an easy-to-interpret quantile criterion. The new method does not need to specify an outcome regression model and is robust for heavy-tailed distribution. The estimation problem corresponds to a nonregular <i>M</i>-estimation problem with both finite and infinite-dimensional nuisance parameters. Employing advanced empirical process techniques, we establish the statistical theory of the estimated parameter indexing the optimal IDR. Furthermore, we prove a novel result that the proposed approach can consistently estimate the optimal value function under mild conditions even when the optimal IDR is nonunique, which happens in the challenging setting of exceptional laws. We also propose a smoothed resampling procedure for inference. The proposed methods are implemented in the R-package QTOCen. We demonstrate the performance of the proposed new methods via extensive Monte Carlo studies and a real data application. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.12853458
title: Transcriptome analysis of two lines of <i>Brassica oleracea</i> in response to early infection with <i>Xanthomonas campestris</i> pv. <i>campestris</i>

description: Black rot, caused by <i>Xanthomonas campestris</i> pv. <i>campestris</i> (Pammel) Dowson (Xcc), is a devastating disease of cruciferous crops worldwide and a threat to the economic production of <i>Brassica oleracea</i> L. in China. Strategies to control this disease are limited. In addition, knowledge of the molecular mechanisms of pathogenicity and host resistance are still only poorly understood. In this study, we performed transcriptomic analyses of the leaves of two contrasting <i>B. oleracea</i> lines (Xcc-resistant line QP07 and Xcc-susceptible line DBP71) to study the early defence response induced by infection with Xcc. We identified 3357 upregulated and 4091 downregulated genes between QP07 and DBP71 at 0, 12, 24, 48 and 96 h post-inoculation (hpi). A functional annotation pathways analysis of the differentially expressed genes indicated that the glucosinolate biosynthetic and catabolic pathways were enhanced, and ROS scavenging, hormonal, receptor-kinase-related genes and nucleotide binding site (NBS)-encoding resistance genes were expressed during the early infection period. In addition, we found that the host plants may respond to Xcc infection by actively regulating photosynthetic energy metabolism. The results provide new insights to help understand the different responses to Xcc in resistant and susceptible host genotypes, and to aid in the development of effective strategies for the prevention of black rot.
DOI: 10.6084/m9.figshare.12853458.v1
title: Transcriptome analysis of two lines of <i>Brassica oleracea</i> in response to early infection with <i>Xanthomonas campestris</i> pv. <i>campestris</i>

description: Black rot, caused by <i>Xanthomonas campestris</i> pv. <i>campestris</i> (Pammel) Dowson (Xcc), is a devastating disease of cruciferous crops worldwide and a threat to the economic production of <i>Brassica oleracea</i> L. in China. Strategies to control this disease are limited. In addition, knowledge of the molecular mechanisms of pathogenicity and host resistance are still only poorly understood. In this study, we performed transcriptomic analyses of the leaves of two contrasting <i>B. oleracea</i> lines (Xcc-resistant line QP07 and Xcc-susceptible line DBP71) to study the early defence response induced by infection with Xcc. We identified 3357 upregulated and 4091 downregulated genes between QP07 and DBP71 at 0, 12, 24, 48 and 96 h post-inoculation (hpi). A functional annotation pathways analysis of the differentially expressed genes indicated that the glucosinolate biosynthetic and catabolic pathways were enhanced, and ROS scavenging, hormonal, receptor-kinase-related genes and nucleotide binding site (NBS)-encoding resistance genes were expressed during the early infection period. In addition, we found that the host plants may respond to Xcc infection by actively regulating photosynthetic energy metabolism. The results provide new insights to help understand the different responses to Xcc in resistant and susceptible host genotypes, and to aid in the development of effective strategies for the prevention of black rot.
DOI: 10.6084/m9.figshare.22814900
title: Additional file 1 of A giant invasive macroprolactinoma with recurrent nasal bleeding as the first clinical presentation: case report and review of literature

description: Additional file 1.
DOI: 10.6084/m9.figshare.22814900.v1
title: Additional file 1 of A giant invasive macroprolactinoma with recurrent nasal bleeding as the first clinical presentation: case report and review of literature

description: Additional file 1.
DOI: 10.6084/m9.figshare.19144932
title: Additional file 2 of Positive H. pylori status predicts better prognosis of non-cardiac gastric cancer patients: results from cohort study and meta-analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.19144932.v1
title: Additional file 2 of Positive H. pylori status predicts better prognosis of non-cardiac gastric cancer patients: results from cohort study and meta-analysis

description: Additional file 2.
DOI: 10.6084/m9.figshare.13902097
title: Transcriptome profiling of different types of human respiratory tract cells infected by SARS-CoV-2 highlight an unique role for inflammatory and interferon response

description: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) at the end of 2019 has caused a large global outbreak and now become a major public health issue. However, there is currently a lack of data underlying how the human host interacts with SARS-CoV-2 virus. In the current study, We performed Venn-analysis, Gene ontology (GO), KEGG pathway analysis and Protein-protein interaction analysis of whole transcriptome studies with the aim of clarifying the genes and pathways potentially altered during human respiratory tract cell infection with SARS-CoV-2. We found 36 overlapping upregulated genes among different types of cells after viral infection. Further functional enrichment analysis revealed these Differential Expressed Genes (DEGs) are most likely involved in biological processes related to inflammatory response and response to cytokine, cell component related to extracellular space and I-kappa B/NF-kappa B complex, molecular function related to protein binding and cytokine activity. KEGG pathways analysis highlighted altered conical and casual pathways related to TNF, NF-kappa B, Cytokine-cytokine receptor interaction and IL-17 signaling pathways during SARS CoV-2 infection with CXCL1, CXCL2, CXCL3, CXCL8, CXCL10, IL32, CX3CL1, CCL20, IRF1, NFKB2 and NFKB1A up-regulated which may explain the inflammatory cytokine storms associated with severe cases of COVID-19.
DOI: 10.6084/m9.figshare.13902097.v1
title: Transcriptome profiling of different types of human respiratory tract cells infected by SARS-CoV-2 highlight an unique role for inflammatory and interferon response

description: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) at the end of 2019 has caused a large global outbreak and now become a major public health issue. However, there is currently a lack of data underlying how the human host interacts with SARS-CoV-2 virus. In the current study, We performed Venn-analysis, Gene ontology (GO), KEGG pathway analysis and Protein-protein interaction analysis of whole transcriptome studies with the aim of clarifying the genes and pathways potentially altered during human respiratory tract cell infection with SARS-CoV-2. We found 36 overlapping upregulated genes among different types of cells after viral infection. Further functional enrichment analysis revealed these Differential Expressed Genes (DEGs) are most likely involved in biological processes related to inflammatory response and response to cytokine, cell component related to extracellular space and I-kappa B/NF-kappa B complex, molecular function related to protein binding and cytokine activity. KEGG pathways analysis highlighted altered conical and casual pathways related to TNF, NF-kappa B, Cytokine-cytokine receptor interaction and IL-17 signaling pathways during SARS CoV-2 infection with CXCL1, CXCL2, CXCL3, CXCL8, CXCL10, IL32, CX3CL1, CCL20, IRF1, NFKB2 and NFKB1A up-regulated which may explain the inflammatory cytokine storms associated with severe cases of COVID-19.
DOI: 10.6084/m9.figshare.22815008
title: Additional file 8 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.22815011
title: Additional file 9 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 9
DOI: 10.6084/m9.figshare.22815011.v1
title: Additional file 9 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 9
DOI: 10.6084/m9.figshare.22814990
title: Additional file 2 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.22815014
title: Additional file 10 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 10
DOI: 10.6084/m9.figshare.22814990.v1
title: Additional file 2 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 2
DOI: 10.6084/m9.figshare.22815008.v1
title: Additional file 8 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 8
DOI: 10.6084/m9.figshare.22815014.v1
title: Additional file 10 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 10
DOI: 10.6084/m9.figshare.22815017
title: Additional file 11 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 11
DOI: 10.6084/m9.figshare.22815017.v1
title: Additional file 11 of Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer

description: Supplementary Material 11
DOI: 10.6084/m9.figshare.12853584
title: Expanding the molecular toolbox for Zygnematophyceae – transient genetic transformation of the desmid <i>Micrasterias radians</i> var. <i>evoluta</i>

description: In the past, various species of the unicellular algal genus <i>Micrasterias</i> (Zygnematophyceae) have been used for research in the fields of cell biology and physiology. Relatively large cell size, highly differentiated cell shape and a remarkable evolutionary position make <i>Micrasterias</i> interesting, especially for cytomorphogenetic studies. However, within this genus a model organism enabling molecular research has not yet been established. <i>Micrasterias radians</i> var. <i>evoluta</i> (W.B.Turner) Krieger allows easy culturing under axenic conditions and performs its whole life cycle <i>in vitro</i> thus fulfilling two important prerequisites for a model organism. In this work resources allowing transient expression of transgenes were developed. First, axenic lines were obtained by the treatment of zygospores with a cocktail of antibiotics followed by germination and regeneration. In order to allow transgene expression we isolated the 5′ -flanking region of the <i>M. radians</i> var. <i>evoluta Actin1</i> gene (<i>MrACT1</i>) and fused it to the green fluorescent protein (GFP). A higher promoter activity compared with various heterologous promoters regarding GFP expression was observed. Transient transgene expression was achieved by polyethylene glycol (PEG)-mediated protoplast transformation, yielding a rate of 3.9% transformed cells per surviving protoplasts. Transgene expression was also achieved by particle bombardment of vegetative cells. Employing the established protocol, a Lifeact-GFP fusion protein for labelling F-actin was expressed, allowing visualization of the actin cytoskeleton in <i>M. radians</i> var. <i>evoluta</i>.
DOI: 10.6084/m9.figshare.22815039
title: Additional file 1 of Fatal, non-fatal burden of cancer in the elderly in China, 2005–2016: a nationwide registry-based study

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.22815039.v1
title: Additional file 1 of Fatal, non-fatal burden of cancer in the elderly in China, 2005–2016: a nationwide registry-based study

description: Supplementary Material 1
DOI: 10.6084/m9.figshare.12853596
title: The released polysaccharide inhibits cell aggregation and biofilm formation in the cyanobacterium <i>Synechocystis</i> sp. PCC 6803

description: Cyanobacteria secrete exopolysaccharide (EPS), which can be intimately associated with the cell surfaces (known as capsular polysaccharide, CPS), or released into the surrounding environment (released polysaccharide, RPS). The aim of this study was to explore the role of EPS in cell aggregation and biofilm formation in the unicellular cyanobacterium <i>Synechocystis</i> sp. strain PCC 6803. Three mutants (Δ<i>sll5043</i>, Δ<i>slr1063</i> and Δ<i>slr1076</i>) were obtained through disrupting three putative glycosyltransferase genes (<i>sll5043</i>, <i>slr1063</i> and <i>slr1076</i>) separately. Decreased contents and altered monosaccharide composition of both RPS and CPS were observed in the three mutants compared with the wild type (WT). RPS from the WT (WT-RPS) had high emulsification activity, while RPSs from the mutants had no emulsification activity. Unlike the WT, the three mutants formed cell aggregates and biofilms. Compared with the WT, the three mutants possessed lower cell hydrophobicity and less negative cell surface charge, which could result from the altered production of CPS. 40 μg ml<sup>–1</sup> WT-RPS significantly decreased cell hydrophobicity of the three mutants, and significantly inhibited cell aggregation and biofilm formation, while the RPS from each mutant itself had no effect on cell hydrophobicity of the mutant, and did not affect cell aggregation and biofilm formation. The inhibitory effect of WT-RPS on cell aggregation and biofilm formation was thus suggested to be related to its ability to reduce cell hydrophobicity. The difference in cell aggregation and biofilm formation between the WT and the three mutants could be related to differences in cell hydrophobicity, cell surface charge and physicochemical properties of RPS. Our results in this study indicated that both CPS and RPS affected cell aggregation and biofilm formation in <i>Synechocystis</i> sp. strain PCC 6803, and WT-RPS inhibited cell aggregation and biofilm formation.
DOI: 10.6084/m9.figshare.12853596.v1
title: The released polysaccharide inhibits cell aggregation and biofilm formation in the cyanobacterium <i>Synechocystis</i> sp. PCC 6803

description: Cyanobacteria secrete exopolysaccharide (EPS), which can be intimately associated with the cell surfaces (known as capsular polysaccharide, CPS), or released into the surrounding environment (released polysaccharide, RPS). The aim of this study was to explore the role of EPS in cell aggregation and biofilm formation in the unicellular cyanobacterium <i>Synechocystis</i> sp. strain PCC 6803. Three mutants (Δ<i>sll5043</i>, Δ<i>slr1063</i> and Δ<i>slr1076</i>) were obtained through disrupting three putative glycosyltransferase genes (<i>sll5043</i>, <i>slr1063</i> and <i>slr1076</i>) separately. Decreased contents and altered monosaccharide composition of both RPS and CPS were observed in the three mutants compared with the wild type (WT). RPS from the WT (WT-RPS) had high emulsification activity, while RPSs from the mutants had no emulsification activity. Unlike the WT, the three mutants formed cell aggregates and biofilms. Compared with the WT, the three mutants possessed lower cell hydrophobicity and less negative cell surface charge, which could result from the altered production of CPS. 40 μg ml<sup>–1</sup> WT-RPS significantly decreased cell hydrophobicity of the three mutants, and significantly inhibited cell aggregation and biofilm formation, while the RPS from each mutant itself had no effect on cell hydrophobicity of the mutant, and did not affect cell aggregation and biofilm formation. The inhibitory effect of WT-RPS on cell aggregation and biofilm formation was thus suggested to be related to its ability to reduce cell hydrophobicity. The difference in cell aggregation and biofilm formation between the WT and the three mutants could be related to differences in cell hydrophobicity, cell surface charge and physicochemical properties of RPS. Our results in this study indicated that both CPS and RPS affected cell aggregation and biofilm formation in <i>Synechocystis</i> sp. strain PCC 6803, and WT-RPS inhibited cell aggregation and biofilm formation.
DOI: 10.6084/m9.figshare.11805039
title: Additional file 10 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 10: GO analysis information of DEGs significantly enriched in 244 biological processes.
DOI: 10.6084/m9.figshare.11805039.v1
title: Additional file 10 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 10: GO analysis information of DEGs significantly enriched in 244 biological processes.
DOI: 10.6084/m9.figshare.11805048
title: Additional file 11 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 11: KEGG pathway analysis of DEGs in mock- and DHAV-3-infected duckling livers.
DOI: 10.6084/m9.figshare.11805048.v1
title: Additional file 11 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 11: KEGG pathway analysis of DEGs in mock- and DHAV-3-infected duckling livers.
DOI: 10.6084/m9.figshare.12853643
title: Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries

description: A newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences available in the GISAID platform as of 5 March 2020. Among them, four genetic clusters, defined as super-spreaders (SSs), could be identified and were found to be responsible for the major outbreaks that subsequently occurred in various countries. SS1 was widely disseminated in Asia and the US, and mainly responsible for outbreaks in the states of Washington and California as well as South Korea, whereas SS4 contributed to the pandemic in Europe. Using the signature mutations of each SS as markers, we further analysed 1539 genome sequences reported after 29 February 2020 and found that 90% of these genomes belonged to SSs, with SS4 being the most dominant. The relative degree of contribution of each SS to the pandemic in different continents was also depicted. Identification of these super-spreaders greatly facilitates development of new strategies to control the transmission of SARS-CoV-2.
DOI: 10.6084/m9.figshare.11805066
title: Additional file 1 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 1: Known miRNAs identified in this study.
DOI: 10.6084/m9.figshare.11805066.v1
title: Additional file 1 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 1: Known miRNAs identified in this study.
DOI: 10.6084/m9.figshare.11805069
title: Additional file 2 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 2: Novel miRNAs identified in this study.
DOI: 10.6084/m9.figshare.22815068
title: Additional file 1 of Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits

description: Additional file 1: Figure S1. Phylogenetic relationships and population structures. Figure S2. Geographical distribution and breeding selection of the haplotype blocks associated with the length of the second internode on chromosome 1A. Figure S3. Geographical distribution and breeding selection of the haplotype blocks associated with the length of the third internode on chromosome 3D. Figure S4. Geographical distribution and breeding selection of the haplotype blocks associated with the length of the fourth internode on chromosome 2A. Figure S5. The evolutionary relationship of the haplotypes for the loci for the length of second internode, third internode, four internode.
DOI: 10.6084/m9.figshare.11805069.v1
title: Additional file 2 of Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

description: Additional file 2: Novel miRNAs identified in this study.