cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7874156
title: Maternal mitochondrial inheritance in two <i>Fusarium</i> pathogens of prickly ash (<i>Zanthoxylum bungeanum</i>) in northern China

description: Mitochondrial inheritance in <i>Fusarium zanthoxyli</i> and <i>F. continuum</i>, two canker-inducing pathogens of prickly ash (<i>Zanthoxylum bungeanum</i>) in northern China, was investigated by genotyping ascospore progeny obtained from laboratory crosses. Polymorphic regions of the mitochondrial genomes (mitogenomes) that contained indels and single-nucleotide polymorphisms (SNPs) were identified via comparative analyses of the complete mitogenomes of the parents used in the intraspecific crosses. A reciprocal genetic cross of <i>F. zanthoxyli</i> NRRL 66714 × NRRL 66285, and a separate cross of <i>F. continuum</i> ♀ NRRL 66286 × ♂ NRRL 66218, revealed that mitochondria were only inherited from the maternal parent. In addition, the reciprocal cross demonstrated that mitochondrial inheritance is not linked to mating type. Gene order in the circular mitogenomes of the prickly ash pathogens was identical to that previously reported for other fusaria and members of the Hypocreales, except that the <i>TRNL</i> tRNAs were duplicated in <i>F. zanthoxyli</i> NRRL 66714. The genomes contained 14 polypeptide-encoding genes involved in oxidative respiration, one intron-encoded ribosomal protein (<i>rps3</i>) gene, two ribosomal RNA (rRNA) genes, and 26–28 tRNA genes. The <i>F. zanthoxyli</i> mitogenomes were 80.9 and 98.7 kb in length, whereas those of <i>F. continuum</i> were considerably shorter and nearly identical in length at 63.4 kb. The significant differences in mitogenome length were primarily due to variable numbers of introns and open reading frames (ORFs) encoding hypothetical proteins.
DOI: 10.6084/m9.figshare.16786812.v1
title: Additional file 1 of Quantitative proteomics by iTRAQ-PRM based reveals the new characterization for gout

description: Additional file 1: Table S1. Details of differentially proteins. Table S2. The mapped signaling pathways of the differentially expressed proteins between AG and control. Table S3. The mapped signaling pathways of the differentially expressed proteins between RG and control. Table S4. The mapped signaling pathways of the differentially expressed proteins between AHU and control. Table S5. The mapped signaling pathways of the differentially expressed proteins between AG and AHU. Table S6. Sheet 1. Information about all candidate peptides of the protein to be validated. Sheet 2. A list of peptides from DDA analysis. Table S7. OLPS-DA VIP score more than 1. Figure S1. Example chromatogram of peptide segments. Supplementary Figure S2. Serum profles of DEPs for the healthy controls (CTL), the patients with acute gout (AG), remission of gout (RG) and asymptomatic hyperuricemia (AHU).
DOI: 10.6084/m9.figshare.16787011.v1
title: LINC00839/miR-144-3p/WTAP (WT1 Associated Protein) axis is involved in regulating hepatocellular carcinoma progression

description: The present work aimed to explore LINC00839 expression level and its function in hepatocellular carcinoma (HCC), and identify the downstream molecular mechanisms. qRT-PCR (Real-Time Quantitative Reverse Transcription PCR) and western blot were employed to detect mRNA and protein levels. Functional investigations were performed by flow cytometric-based apoptosis assay, CCK8 (Cell Counting Kit-8) assay, clone formation assay, Transwell migration and invasion assay. Functional interactions between LINC00839 and miR-144-3p or miR-144-3p and WTAP were validated by dual luciferase reporter assay. siRNA (small interfering RNA) was used for LINC00839 silencing, and microRNA mimic or inhibitor were employed to modulate miR-144-3p activity. LINC00839 was upregulated in HCC cells and tissues. Silencing LINC00839 suppressed the proliferation, invasion, migration of HCC cells and induced apoptosis. Additionally, LINC00839 served as a sponge to negatively impact on miR-144-3p activity, which contributed to the high expression of WTAP (WT1 Associated Protein) and the malignant phenotype of HCC cells. Our study revealed an oncogenic role of LINC00839 in HCC, and identified miR-144-3p/WTAP axis as downstream effectors mediating the oncogenic function of LINC00839. LINC00839 might serve as a potential therapeutic target and prognostic marker for HCC.
DOI: 10.6084/m9.figshare.16786968
title: Additional file 1 of Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

description: Additional file 1.
DOI: 10.6084/m9.figshare.16786977
title: Additional file 4 of Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

description: Additional file 4.
DOI: 10.6084/m9.figshare.16786812
title: Additional file 1 of Quantitative proteomics by iTRAQ-PRM based reveals the new characterization for gout

description: Additional file 1: Table S1. Details of differentially proteins. Table S2. The mapped signaling pathways of the differentially expressed proteins between AG and control. Table S3. The mapped signaling pathways of the differentially expressed proteins between RG and control. Table S4. The mapped signaling pathways of the differentially expressed proteins between AHU and control. Table S5. The mapped signaling pathways of the differentially expressed proteins between AG and AHU. Table S6. Sheet 1. Information about all candidate peptides of the protein to be validated. Sheet 2. A list of peptides from DDA analysis. Table S7. OLPS-DA VIP score more than 1. Figure S1. Example chromatogram of peptide segments. Supplementary Figure S2. Serum profles of DEPs for the healthy controls (CTL), the patients with acute gout (AG), remission of gout (RG) and asymptomatic hyperuricemia (AHU).
DOI: 10.6084/m9.figshare.7874156.v1
title: Maternal mitochondrial inheritance in two <i>Fusarium</i> pathogens of prickly ash (<i>Zanthoxylum bungeanum</i>) in northern China

description: Mitochondrial inheritance in <i>Fusarium zanthoxyli</i> and <i>F. continuum</i>, two canker-inducing pathogens of prickly ash (<i>Zanthoxylum bungeanum</i>) in northern China, was investigated by genotyping ascospore progeny obtained from laboratory crosses. Polymorphic regions of the mitochondrial genomes (mitogenomes) that contained indels and single-nucleotide polymorphisms (SNPs) were identified via comparative analyses of the complete mitogenomes of the parents used in the intraspecific crosses. A reciprocal genetic cross of <i>F. zanthoxyli</i> NRRL 66714 × NRRL 66285, and a separate cross of <i>F. continuum</i> ♀ NRRL 66286 × ♂ NRRL 66218, revealed that mitochondria were only inherited from the maternal parent. In addition, the reciprocal cross demonstrated that mitochondrial inheritance is not linked to mating type. Gene order in the circular mitogenomes of the prickly ash pathogens was identical to that previously reported for other fusaria and members of the Hypocreales, except that the <i>TRNL</i> tRNAs were duplicated in <i>F. zanthoxyli</i> NRRL 66714. The genomes contained 14 polypeptide-encoding genes involved in oxidative respiration, one intron-encoded ribosomal protein (<i>rps3</i>) gene, two ribosomal RNA (rRNA) genes, and 26–28 tRNA genes. The <i>F. zanthoxyli</i> mitogenomes were 80.9 and 98.7 kb in length, whereas those of <i>F. continuum</i> were considerably shorter and nearly identical in length at 63.4 kb. The significant differences in mitogenome length were primarily due to variable numbers of introns and open reading frames (ORFs) encoding hypothetical proteins.
DOI: 10.6084/m9.figshare.16786947.v1
title: Additional file 10 of Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

description: Additional file 10.
DOI: 10.6084/m9.figshare.16786980
title: Additional file 5 of Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

description: Additional file 5.
DOI: 10.6084/m9.figshare.16786980.v1
title: Additional file 5 of Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

description: Additional file 5.
DOI: 10.6084/m9.figshare.16786977.v1
title: Additional file 4 of Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction

description: Additional file 4.
DOI: 10.6084/m9.figshare.12593009
title: Additional file 4 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 4: Table S4. 11 OS-related DEAS events determined by LASSO regression.
DOI: 10.6084/m9.figshare.12593015
title: Additional file 6 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 6: Table S6. Six tumor-related SFs determined by differential analysis.
DOI: 10.6084/m9.figshare.12593015.v1
title: Additional file 6 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 6: Table S6. Six tumor-related SFs determined by differential analysis.
DOI: 10.6084/m9.figshare.16786689
title: Additional file 6 of Zinc-mediated activation of CREB pathway in proliferation of pulmonary artery smooth muscle cells in pulmonary hypertension

description: Additional file 5: Table S1. The differentially expressed phosphatases in comparison of MCT-treatment 4 weeks with control.
DOI: 10.6084/m9.figshare.12593006
title: Additional file 3 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 3: Table S3. 96 DFS-related DEAS events determined by univariate Cox regression.
DOI: 10.6084/m9.figshare.12593009.v1
title: Additional file 4 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 4: Table S4. 11 OS-related DEAS events determined by LASSO regression.
DOI: 10.6084/m9.figshare.12593000.v1
title: Additional file 1 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 1: Table S1. 1041 DEASs determined by comparing HP- GC to adjacent normal tissues.
DOI: 10.6084/m9.figshare.16786857.v1
title: Additional file 1 of Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer

description: Additional file 1: Supplementary Tables S1-S5.
DOI: 10.6084/m9.figshare.12593012
title: Additional file 5 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 5: Table S5. 13 DFS-related DEAS events determined by LASSO regression.
DOI: 10.6084/m9.figshare.12593003
title: Additional file 2 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 2: Table S2. 67 OS-related DEAS events determined by univariate Cox regression.
DOI: 10.6084/m9.figshare.12593003.v1
title: Additional file 2 of Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance

description: Additional file 2: Table S2. 67 OS-related DEAS events determined by univariate Cox regression.
DOI: 10.6084/m9.figshare.21506045
title: RESEARCH ON WIND PRESSURE DISTRIBUTION OF PLASTIC GREENHOUSES IN VALLEY TOPOGRAPHY

description: ABSTRACT As the wind pressure distribution on plastic greenhouses in valley areas is different from that of greenhouses on plains, it is necessary to find out the variation trend of the wind pressure coefficient on greenhouses in the valley areas. Based on the ‘Realizable k-e turbulence’ model, the wind pressure characteristics on plastic greenhouses located in valley and plain areas are studied by using the verified numerical simulation method. The wind pressures on greenhouses and the corresponding fitting formula are obtained for different distances between the greenhouse and the foot of the mountain with a 0-degree wind angle. The results show that, with an increase of distance to the mountain, the positive wind pressure on the windward side of a plastic greenhouse increases and the negative wind pressure on the leeward side, roof surface and crosswind sides of the greenhouse decreases. The results from the proposed formulae are very close to those derived from the numerical simulation method, and the relative errors are all within 10%. The influence of canyon wind on the wind pressure distribution on plastic greenhouses should be considered in the design. This research can provide a reference for the wind resistance design of plastic greenhouses built in valley areas.
DOI: 10.6084/m9.figshare.19409000.v1
title: The distribution, behavior, and release of macro- and micro-size plastic wastes in solid waste disposal sites

description: Sanitary landfills and uncontrolled dumpsites are plastic wastes (PWs) reservoirs containing ∼60% of all the plastics ever made, amounting to 5,000 × 10<sup>6</sup> tons as of 2017. The distribution, long-term behavior, and release of macro- and microplastics (MPs) from disposal sites are critical to global plastics pollution, but are poorly understood and lack systematic assessments. We review comprehensively the available knowledge in the three aspects herein. The spatial and temporal distribution of PW in 616 municipal solid waste (MSW) samples retrieved from 275 disposal sites in 56 countries are summarized. The weight percentages of PW (%PW) generally decrease with increasing year of disposal and disposal depth. Other influential factors are disposal duration and country income level. The %PW values in different disposal sites show high regionality and spatial variability and heterogeneity. Disposal sites mostly have harsh temperature and stress, reactive liquids, and microbial activities, which are conducive to long-term processes of PW and MPs. The major processes are chemical degradation, dissolution, leaching and adsorption, biological degradation, mechanical wearing, pneumatic and hydrological transport and deposition, and conglomeration. PW leaves disposal sites via recycling, scavenging, mining, wind and surface runoff, coastal erosion and flooding, and slope failure. The release and removal pathways of PW from disposal sites have been recognized only qualitatively. In addition, the sources, presences, and secondary generation of MPs in disposal sites have been studied occasionally, whereas the transport and fate of MPs within and from disposal sites remain largely unstudied.
DOI: 10.6084/m9.figshare.16786857
title: Additional file 1 of Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer

description: Additional file 1: Supplementary Tables S1-S5.
DOI: 10.6084/m9.figshare.12592748
title: Additional file 10 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 10: Table S6. Primers for qRT-PCR.
DOI: 10.6084/m9.figshare.12592748.v1
title: Additional file 10 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 10: Table S6. Primers for qRT-PCR.
DOI: 10.6084/m9.figshare.12592763
title: Additional file 5 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 5: Table S1. The statistics for the sequencing data and alignment with the reference genome.
DOI: 10.6084/m9.figshare.1582725
title: FGFR3/fibroblast growth factor receptor 3 inhibits autophagy through decreasing the ATG12–ATG5 conjugate, leading to the delay of cartilage development in achondroplasia

description: FGFR3 (fibroblast growth factor receptor 3) is a negative regulator of endochondral ossification. Gain-of-function mutations in <i>FGFR3</i> are responsible for achondroplasia, the most common genetic form of dwarfism in humans. Autophagy, an evolutionarily conserved catabolic process, maintains chondrocyte viability in the growth plate under stress conditions, such as hypoxia and nutritional deficiencies. However, the role of autophagy and its underlying molecular mechanisms in achondroplasia remain elusive. In this study, we found activated FGFR3 signaling inhibited autophagic activity in chondrocytes, both in vivo and in vitro. By employing an embryonic bone culture system, we demonstrated that treatment with autophagy inhibitor 3-MA or chloroquine led to cartilage growth retardation, which mimics the effect of activated-FGFR3 signaling on chondrogenesis. Furthermore, we found that FGFR3 interacted with ATG12–ATG5 conjugate by binding to ATG5. More intriguingly, FGFR3 signaling was found to decrease the protein level of ATG12–ATG5 conjugate. Consistently, using in vitro chondrogenic differentiation assay system, we showed that the ATG12–ATG5 conjugate was essential for the viability and differentiation of chondrocytes. Transient transfection of ATG5 partially rescued FGFR3-mediated inhibition on chondrocyte viability and differentiation. Our findings reveal that FGFR3 inhibits the autophagic activity by decreasing the ATG12–ATG5 conjugate level, which may play an essential role in the pathogenesis of achondroplasia.
DOI: 10.6084/m9.figshare.12592775
title: Additional file 9 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 9: Table S5. The expression levels and annotations of genes in the QTL regions.
DOI: 10.6084/m9.figshare.12592775.v1
title: Additional file 9 of New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

description: Additional file 9: Table S5. The expression levels and annotations of genes in the QTL regions.
DOI: 10.6084/m9.figshare.21505800
title: XRD数据.xlsx

description: This is  original data.
DOI: 10.21942/uva.25061858.v3
title: CW measurement for Drift Detection

description: Partial CW long measurement used for Drift Detection
DOI: 10.6084/m9.figshare.25145516
title: Revisão dos autores

description: Revisão dos autores sobre os artigos
DOI: 10.6084/m9.figshare.25145516.v1
title: Revisão dos autores

description: Revisão dos autores sobre os artigos
DOI: 10.6084/m9.figshare.22555440
title: miR-100-5p is upregulated in multiple myeloma and involves in the pathogenesis of multiple myeloma through targeting MTMR3

description: MicroRNA (miRNA) is a kind of highly conserved single-stranded small endogenous non-coding RNA associated with multiple diseases, particularly cancer. The miRNAs expression profile in multiple myeloma (MM) has been barely elucidated. The miRNAs expression profiles in bone marrow plasma cells of 5 MM individuals and 5 iron-deficiency anemia volunteers were analyzed using RNA-sequencing. Quantitative polymerase chain reaction (QPCR) was performed to validate the expression of selected miR-100-5p. The biological function of selected miRNA was predicated by bioinformatics analysis. Finally, the function of miR-100-5p and its target on MM cells were evaluated. MiRNA-sequencing showed that miR-100-5p was obviously upregulated in MM patients, which was further validated in an expanded cohort. Receiver operating characteristic curve analysis characterized miR-100-5p as a valuable biomarker of MM. Bioinformatics analysis predicted that miR-100-5p is targeted to CLDN11, ICMT, MTMR3, RASGRP3, and SMARCA5, and their low expression are associated with poor prognosis of MM patients. Kyoto encyclopedia of genes and genomes analysis suggested that the major interacting proteins of these five targets are mainly enriched in inositol phosphate metabolism and phosphatidylinositol signaling system pathway. <i>In vitro</i> study showed that miR-100-5p inhibition promoted the expression of these targets, especially MTMR3. In addition, miR-100-5p inhibition declined living number and metastasis, whereas promoted apoptosis of RPMI 8226 and U266 MM cells. The function of miR-100-5p inhibition was weakened by MTMR3 inhibition. These results indicates that miR-100-5p is a promising biomarker for MM, and that it may involve in the pathogenesis of MM by targeting MTMR3.
DOI: 10.6084/m9.figshare.22555440.v1
title: miR-100-5p is upregulated in multiple myeloma and involves in the pathogenesis of multiple myeloma through targeting MTMR3

description: MicroRNA (miRNA) is a kind of highly conserved single-stranded small endogenous non-coding RNA associated with multiple diseases, particularly cancer. The miRNAs expression profile in multiple myeloma (MM) has been barely elucidated. The miRNAs expression profiles in bone marrow plasma cells of 5 MM individuals and 5 iron-deficiency anemia volunteers were analyzed using RNA-sequencing. Quantitative polymerase chain reaction (QPCR) was performed to validate the expression of selected miR-100-5p. The biological function of selected miRNA was predicated by bioinformatics analysis. Finally, the function of miR-100-5p and its target on MM cells were evaluated. MiRNA-sequencing showed that miR-100-5p was obviously upregulated in MM patients, which was further validated in an expanded cohort. Receiver operating characteristic curve analysis characterized miR-100-5p as a valuable biomarker of MM. Bioinformatics analysis predicted that miR-100-5p is targeted to CLDN11, ICMT, MTMR3, RASGRP3, and SMARCA5, and their low expression are associated with poor prognosis of MM patients. Kyoto encyclopedia of genes and genomes analysis suggested that the major interacting proteins of these five targets are mainly enriched in inositol phosphate metabolism and phosphatidylinositol signaling system pathway. <i>In vitro</i> study showed that miR-100-5p inhibition promoted the expression of these targets, especially MTMR3. In addition, miR-100-5p inhibition declined living number and metastasis, whereas promoted apoptosis of RPMI 8226 and U266 MM cells. The function of miR-100-5p inhibition was weakened by MTMR3 inhibition. These results indicates that miR-100-5p is a promising biomarker for MM, and that it may involve in the pathogenesis of MM by targeting MTMR3.
DOI: 10.6084/m9.figshare.12592946
title: Additional file 8 of Identification of vital candidate microRNA/mRNA pairs regulating ovule development using high-throughput sequencing in hazel

description: Additional file 8 Table S7 DEmRNAs of DEmiRNAs
DOI: 10.15156/bio/sh059843.07fu
title: SH059843.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.