cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16960618.v1
title: Additional file 2 of Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis

description: Additional file 2: Table S1. GO enrichment of chrysanthemum flowers. Table S2. KEGG pathways enriched in the chrysanthemum flowers. Table S3. List of flavonoid biosynthesis-related DEGs. Table S4. List of Phenylpropanoid biosynthesis-related DEGs. Table S5. List of fatty acid and unsaturated fatty acid biosynthesis-related DEGs. Table S6. List of cell wall metabolism-related DEGs. Table S7. List of TF-related DEGs. Table S8. List of the quantitative primers for qRT-PCR in this study. Table S9. List of hormone-related DEGs. Table S10. List of photosynthesis-related DEGs.
DOI: 10.6084/m9.figshare.19581963
title: Additional file 13 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 13. 12864_2022_8515_MOESM13_ESM.xlsx.
DOI: 10.6084/m9.figshare.20626409
title: Additional file 2 of Circulating exosomal mRNA signatures for the early diagnosis of clear cell renal cell carcinoma

description: Additional file 2: Table S1. Demographic andclinical characteristics of participants with benign solid and cystic masses. Table S2. List of primers and probes. Table S3. List of circulating exosomaldysregulated transcripts between clear cell renal cell carcinoma (ccRCC)patients and healthy controls.
DOI: 10.6084/m9.figshare.20626406
title: Additional file 1 of Circulating exosomal mRNA signatures for the early diagnosis of clear cell renal cell carcinoma

description: Additional file 1: Fig. S1. Quality control ofexosome isolation and verification. Fig.S2. Circulating exosomal RNA screening and testing. Fig. S3. The performance of candidate emRNAs for screeninglocalized clear cell renal cell carcinoma (ccRCC) patients from healthycontrols and differentiating ccRCCs from patients with benign renal masses. Fig. S4. AUC of the signature derivedto distinguish ccRCC from healthy controls for ccRCC versus benign renal masses(AUC = 0.559).
DOI: 10.6084/m9.figshare.6999161.v1
title: Additional file 1: of Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015

description: Table S1. The RNA quality for each sample. (XLSX 8 kb)
DOI: 10.6084/m9.figshare.20106366.v1
title: Substance P promotes the progression of bronchial asthma through activating the PI3K/AKT/NF-κB pathway mediated cellular inflammation and pyroptotic cell death in bronchial epithelial cells

description: NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome-mediated pyroptotic cell death and inflammation contribute to the pathogenesis of bronchial asthma, and it is reported that Substance P (SP) plays important role in the process, however, the detailed molecular mechanisms by which SP participates in the aggravation of bronchial asthma have not been fully studied. Here, our clinical data showed that SP and its receptor Neurokinin-1 receptor (NK1R) were significantly elevated in the plasma and peripheral blood mononuclear cell (PBMC) collected from patients with bronchial asthma, and further pre-clinical experiments evidenced that SP suppressed cell viability, accelerated lactate dehydrogenase (LDH) release, and upregulated ASC, Caspase-1, NLRP3, IL-1β and IL-18 to promote pyroptotic cell death and cellular inflammation in the human bronchial epithelial cells and asthmatic mice models <i>in vitro</i> and <i>in vivo</i>. Interestingly, SP-induced pyroptotic cell death was reversed by NK1R inhibitor L732138. Then, we uncovered the underlying mechanisms, and found that SP activated the downstream PI3K/AKT/NF-κB signal pathway in a NK1R-dependent manner, and blockage of this pathway by both PI3K inhibitor (LY294002) and NF-κB inhibitor (MG132) reversed SP-induced pyroptotic cell death and recovered cell viability in bronchial epithelial cells. Collectively, we concluded that SP interacted with its receptor NK1R to activate the PI3K/AKT/NF-κB pathway, which further triggered NLRP3-mediated pyroptotic cell death in the bronchial epithelial cells, resulting in the aggravation of bronchial asthma.
DOI: 10.6084/m9.figshare.21679294
title: Redo Total Aortic Arch Replacement in Patients with Aortic Dissection After Open-Heart Surgery and Long-Term Follow-Up Results

description: ABSTRACT Introduction: The objectives of this study were to investigate the main treatment strategies and long-term follow-up results of aortic dissection surgery after open-heart surgery (ADSOHS) and to analyze the risk factors that cause ADSOHS. Methods: One hundred thirty-seven patients with ADSOHS hospitalized in our hospital from January 2009 to December 2018 were selected as the research object. Long-term follow-up results, complications, mortality, and changes of cardiac function before and after operation were used to explore the value of Sun’s operation. Results: The length of stay in intensive care unit of these 137 patients ranged from 9.5 to 623.75 hours (average of 76.41±97.29 hours), auxiliary ventilation time ranged from 6.0 to 259.83 hours (average of 46.16±55.59 hours), and hospital stay ranged from six to 85 days (average of 25.06±13.04 days). There were seven cases of postoperative low cardiac output, 18 cases of coma and stroke, and six cases of transient neurological dysfunction. A total of 33 patients died; 19 patients died during the perioperative period, 18 died during Sun’s operation and one died during other operation; and 14 patients died during follow-up (January 2021), 12 cases of Sun’s operation and two cases of other operations. Conclusion: ADSOHS treatment strategy is of high application value, and the risk of neurological complications and mortality is low. The main risk factors are postoperative low cardiac output, coma, stroke, and transient neurological dysfunction. The extracorporeal circulation time is relatively long. Short- and long-term follow-up effects are good, and it is worthy of clinical promotion.
DOI: 10.6084/m9.figshare.20626409.v1
title: Additional file 2 of Circulating exosomal mRNA signatures for the early diagnosis of clear cell renal cell carcinoma

description: Additional file 2: Table S1. Demographic andclinical characteristics of participants with benign solid and cystic masses. Table S2. List of primers and probes. Table S3. List of circulating exosomaldysregulated transcripts between clear cell renal cell carcinoma (ccRCC)patients and healthy controls.
DOI: 10.6084/m9.figshare.21679294.v1
title: Redo Total Aortic Arch Replacement in Patients with Aortic Dissection After Open-Heart Surgery and Long-Term Follow-Up Results

description: ABSTRACT Introduction: The objectives of this study were to investigate the main treatment strategies and long-term follow-up results of aortic dissection surgery after open-heart surgery (ADSOHS) and to analyze the risk factors that cause ADSOHS. Methods: One hundred thirty-seven patients with ADSOHS hospitalized in our hospital from January 2009 to December 2018 were selected as the research object. Long-term follow-up results, complications, mortality, and changes of cardiac function before and after operation were used to explore the value of Sun’s operation. Results: The length of stay in intensive care unit of these 137 patients ranged from 9.5 to 623.75 hours (average of 76.41±97.29 hours), auxiliary ventilation time ranged from 6.0 to 259.83 hours (average of 46.16±55.59 hours), and hospital stay ranged from six to 85 days (average of 25.06±13.04 days). There were seven cases of postoperative low cardiac output, 18 cases of coma and stroke, and six cases of transient neurological dysfunction. A total of 33 patients died; 19 patients died during the perioperative period, 18 died during Sun’s operation and one died during other operation; and 14 patients died during follow-up (January 2021), 12 cases of Sun’s operation and two cases of other operations. Conclusion: ADSOHS treatment strategy is of high application value, and the risk of neurological complications and mortality is low. The main risk factors are postoperative low cardiac output, coma, stroke, and transient neurological dysfunction. The extracorporeal circulation time is relatively long. Short- and long-term follow-up effects are good, and it is worthy of clinical promotion.
DOI: 10.6084/m9.figshare.15041287.v1
title: Additional file 4 of Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

description: Additional file 4. Table S3. Antibiotics and corresponding concentrations used for each conjugation pair.
DOI: 10.6084/m9.figshare.20626424.v1
title: Additional file 1 of Proteomics-based evaluation of the mechanism underlying vascular injury via DNA interstrand crosslinks, glutathione perturbation, mitogen-activated protein kinase, and Wnt and ErbB signaling pathways induced by crotonaldehyde

description: Additional file 1: Table S1. Quantitative analysis of total proteins by TMT-based proteomics analysis.
DOI: 10.6084/m9.figshare.15041287
title: Additional file 4 of Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

description: Additional file 4. Table S3. Antibiotics and corresponding concentrations used for each conjugation pair.
DOI: 10.6084/m9.figshare.15041290.v1
title: Additional file 5 of Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

description: Additional file 5. Table S4. NCBI accession numbers and genetic characteristics of 2608 K. pneumoniae plasmids.
DOI: 10.5281/zenodo.10000775
title: Metallic nickel pillar X-ray spectral ptychographic dataset

description: This dataset was acquired at the SWING beamline at the French synchrotron SOLEIL. The dataset was obtained by conducting spectral 2D X-ray ptychography on a 7-micron diameter metallic nickel pillar. An energy scan was performed from 8.3 KeV to 8.4 KeV with a 1 eV step, including the resonant energy of nickel at 8.333 KeV. For each energy acquisition, the ptychographic scanning parameters consisted of 242 diffraction patterns from a field of view of 14x12 µm², with an exposure time of 100 ms per point. The ptychographic reconstruction was carried out using the PtychoShelves Matlab software package, involving 200 iterations of the difference map (DM) algorithm, followed by 100 iterations of the maximum likelihood (ML) algorithm.
DOI: 10.5281/zenodo.10000776
title: Metallic nickel pillar X-ray spectral ptychographic dataset

description: This dataset was acquired at the SWING beamline at the French synchrotron SOLEIL. The dataset was obtained by conducting spectral 2D X-ray ptychography on a 7-micron diameter metallic nickel pillar. An energy scan was performed from 8.3 KeV to 8.4 KeV with a 1 eV step, including the resonant energy of nickel at 8.333 KeV. For each energy acquisition, the ptychographic scanning parameters consisted of 242 diffraction patterns from a field of view of 14x12 µm², with an exposure time of 100 ms per point. The ptychographic reconstruction was carried out using the PtychoShelves Matlab software package, involving 200 iterations of the difference map (DM) algorithm, followed by 100 iterations of the maximum likelihood (ML) algorithm.
DOI: 10.6084/m9.figshare.20626427
title: Additional file 2 of Proteomics-based evaluation of the mechanism underlying vascular injury via DNA interstrand crosslinks, glutathione perturbation, mitogen-activated protein kinase, and Wnt and ErbB signaling pathways induced by crotonaldehyde

description: Additional file 2: Table S2. Identification of total protein by TMT- based proteomics analysis.
DOI: 10.6084/m9.figshare.19581990.v1
title: Additional file 9 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 9. 12864_2022_8515_MOESM9_ESM.xlsx.
DOI: 10.6084/m9.figshare.14339195
title: Novel insights into clear cell renal cell carcinoma prognosis by comprehensive characterization of aberrant alternative splicing signature: a study based on large-scale sequencing data

description: Clear cell renal cell carcinoma (ccRCC) is the most common type with poor prognosis in kidney tumor. Growing evidence has indicated that aberrant alternative splicing (AS) events are efficacious signatures for tumor prognosis prediction and therapeutic targets. However, the detailed roles of AS events in ccRCC are largely unknown. In our study, level 3 RNA-seq data was acquired from The Cancer Genome Atlas dataset and corresponding AS profiles were detected with the assistance of SpliceSeq software. A total of 2100 aberrant survival-associated AS events were identified via differential expression and univariate cox regression analysis. The final prognostic panel formed by 17 specific events was developed by stepwise least absolute shrinkage and selection operator (LASSO) penalty, with the area under curve (AUC) values of receiver operator characteristic (ROC) curves keeping above 0.7 spanning 1 year to 5 years. And the results from functional enrichment analyses are unanimous that autophagy could be a potential mechanism of splicing regulation in ccRCC. Furthermore, splicing regulatory network was constructed via Spearman correlation between splicing factors and AS events. Finally, unsupervised clustering analysis revealed three clusters with distinct survival patterns, and associated with specific clinicopathological phenotypes. In overall, we developed a robust and individualized predictive model based on large-scale sequencing data. The identified AS events and splicing network may be valuable in deciphering the crucial posttranscriptional mechanisms on tumorigenesis of ccRCC.
DOI: 10.6084/m9.figshare.19581954.v1
title: Additional file 10 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 10. 12864_2022_8515_MOESM10_ESM.xlsx.
DOI: 10.15156/bio/sh1177489.09fu
title: SH1177489.09FU

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.
DOI: 10.15156/bio/sh1177490.09fu
title: SH1177490.09FU

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.
DOI: 10.15156/bio/sh1177491.09fu
title: SH1177491.09FU

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.
DOI: 10.15156/bio/sh1177492.09fu
title: SH1177492.09FU

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.
DOI: 10.15156/bio/sh1177493.09fu
title: SH1177493.09FU

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.
DOI: 10.15156/bio/sh1177494.09fu
title: SH1177494.09FU

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.
DOI: 10.15156/bio/sh1177495.09fu
title: SH1177495.09FU

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.
DOI: 10.15156/bio/sh1177496.09fu
title: SH1177496.09FU

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.