cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19134250.v1
title: CITEMO<sup>XMBD</sup>: A flexible single-cell multimodal omics analysis framework to reveal the heterogeneity of immune cells

description: Simultaneous measurement of multiple modalities in single-cell analysis, represented by CITE-seq, is a promising approach to link transcriptional changes to cellular phenotype and function, requiring new computational methods to define cellular subtypes and states based on multiple data types. Here, we design a flexible single-cell multimodal analysis framework, called CITEMO, to integrate the transcriptome and antibody-derived tags (ADT) data to capture cell heterogeneity from the multi omics perspective. CITEMO uses Principal Component Analysis (PCA) to obtain a low-dimensional representation of the transcriptome and ADT, respectively, and then employs PCA again to integrate these low-dimensional multimodal data for downstream analysis. To investigate the effectiveness of the CITEMO framework, we apply CITEMO to analyse the cell subtypes of Cord Blood Mononuclear Cells (CBMC) samples. Results show that the CITEMO framework can comprehensively analyse single-cell multimodal samples and accurately identify cell subtypes. Besides, we find some specific immune cells that co-express multiple ADT markers. To better describe the co-expression phenomenon, we introduce the co-expression entropy to measure the heterogeneous distribution of the ADT combinations. To further validate the robustness of the CITEMO framework, we analyse Human Bone Marrow Cell (HBMC) samples and identify different states of the same cell type. CITEMO has an excellent performance in identifying cell subtypes and states for multimodal omics data. We suggest that the flexible design idea of CITEMO can be an inspiration for other single-cell multimodal tasks. The complete source code and dataset of the CITEMO framework can be obtained from https://github.com/studentiz/CITEMO.
DOI: 10.6084/m9.figshare.9697070.v1
title: Effect of Electric Pulse Treatment on the Corrosion Resistance of HAl52-2 Aluminum Brass

description: In this work, the effects of electric pulse treatment (EPT) on the corrosion resistance of HAl52-2 aluminum brass has been investigated using electrochemical workstation, scanning electron microscope and X-ray diffraction. The results have shown that after EPT, the corrosion potential increased and the corrosion current density decreased. At the same time, the diameter of the capacitive reactance arc of the HAl52-2 aluminum brass after EPT was 5 ~ 6 times of the original sample, and the thickness of dezincification layer was reduced from 59.2 µm to 50.2 µm by 84.8%. The aluminum brass alloy with EPT has demonstrated better corrosion resistance of than the original sample.
DOI: 10.25582/data.2023-01.2709550/2305133
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709983/2305134
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.7599944
title: Supplementary material from Liquid phase separation in undercooled Cu–Co alloys under the influence of static magnetic fields

description: Measured radii and normalzied frequency of Co-rich droplets of phase-separated Cu84Co16 samples
DOI: 10.6084/m9.figshare.7599944.v1
title: Supplementary material from Liquid phase separation in undercooled Cu–Co alloys under the influence of static magnetic fields

description: Measured radii and normalzied frequency of Co-rich droplets of phase-separated Cu84Co16 samples
DOI: 10.6084/m9.figshare.17037132
title: Additional file 1 of Artificial exosomes mediated spatiotemporal-resolved and targeted delivery of epigenetic inhibitors

description: Additional file 1: Appendix 1. Proteomics analysis of the exosome membrane proteins on different cell lines. M1-EM, exosomes derived from M1 macrophages; R-EM, exosomes derived from RAW264.7 cells; LLC cell, exosomes derived from LLC cells.
DOI: 10.25582/data.2023-02.2732221/2305135
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.17037132.v1
title: Additional file 1 of Artificial exosomes mediated spatiotemporal-resolved and targeted delivery of epigenetic inhibitors

description: Additional file 1: Appendix 1. Proteomics analysis of the exosome membrane proteins on different cell lines. M1-EM, exosomes derived from M1 macrophages; R-EM, exosomes derived from RAW264.7 cells; LLC cell, exosomes derived from LLC cells.
DOI: 10.6084/m9.figshare.7075661.v1
title: Preparation and Growth Characterization of Al2Cu Phase Crystal with the Single Orientation Under Directional Solidification

description: Through decreasing the sample size, the regular faceted rectangular Al2Cu phase crystal was prepared under directional solidification. Effects of sample size on the microstructure morphologies and orientations of intermetallic Al2Cu phase crystal growth at 10 µm/s have been characterized and investigated. The transverse-section microstructure of primary Al2Cu phase crystal transited from L-shaped pattern to regular faceted rectangular pattern with a single preferred orientation at [001] direction with sample size decreasing. By using the serial sectioning technique, the three-dimensional (3D) microstructure of Al2Cu phase in 0.45 mm sample was observed as rectangular parallelepiped. Moreover, the faceted interfaces of Al2Cu phase crystal were determined as {110} planes. Based on growth characteristics of the Al2Cu phase crystal, a growth mode in different sizes samples under directional solidification was proposed. The experimental results show that a regular microstructure with preferred single orientation can be achieved in small-size sample during directional solidification.
DOI: 10.6084/m9.figshare.7075661
title: Preparation and Growth Characterization of Al2Cu Phase Crystal with the Single Orientation Under Directional Solidification

description: Through decreasing the sample size, the regular faceted rectangular Al2Cu phase crystal was prepared under directional solidification. Effects of sample size on the microstructure morphologies and orientations of intermetallic Al2Cu phase crystal growth at 10 µm/s have been characterized and investigated. The transverse-section microstructure of primary Al2Cu phase crystal transited from L-shaped pattern to regular faceted rectangular pattern with a single preferred orientation at [001] direction with sample size decreasing. By using the serial sectioning technique, the three-dimensional (3D) microstructure of Al2Cu phase in 0.45 mm sample was observed as rectangular parallelepiped. Moreover, the faceted interfaces of Al2Cu phase crystal were determined as {110} planes. Based on growth characteristics of the Al2Cu phase crystal, a growth mode in different sizes samples under directional solidification was proposed. The experimental results show that a regular microstructure with preferred single orientation can be achieved in small-size sample during directional solidification.
DOI: 10.6084/m9.figshare.17037138
title: Additional file 2 of Artificial exosomes mediated spatiotemporal-resolved and targeted delivery of epigenetic inhibitors

description: Additional file 2: Appendix 2. Proteomics analysis of the upregulated membrane proteins of the exosomes derived from M1 macrophages, compared with the one from RAW264.7 cells. M1-EM, exosomes derived from M1 macrophages; REM, exosomes derived from RAW264.7 cells.
DOI: 10.25582/data.2023-02.2732661/2305136
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.17037138.v1
title: Additional file 2 of Artificial exosomes mediated spatiotemporal-resolved and targeted delivery of epigenetic inhibitors

description: Additional file 2: Appendix 2. Proteomics analysis of the upregulated membrane proteins of the exosomes derived from M1 macrophages, compared with the one from RAW264.7 cells. M1-EM, exosomes derived from M1 macrophages; REM, exosomes derived from RAW264.7 cells.
DOI: 10.6084/m9.figshare.17037144
title: Additional file 3 of Artificial exosomes mediated spatiotemporal-resolved and targeted delivery of epigenetic inhibitors

description: Additional file 3: Appendix 3. Proteomics analysis of the newly created membrane proteins of the exosomes derived from M1 macrophages, compared with the one from RAW264.7 cells. M1-EM, exosomes derived from M1 macrophages; REM, exosomes derived from RAW264.7 cells.
DOI: 10.25582/data.2023-02.2733242/2305137
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.17037144.v1
title: Additional file 3 of Artificial exosomes mediated spatiotemporal-resolved and targeted delivery of epigenetic inhibitors

description: Additional file 3: Appendix 3. Proteomics analysis of the newly created membrane proteins of the exosomes derived from M1 macrophages, compared with the one from RAW264.7 cells. M1-EM, exosomes derived from M1 macrophages; REM, exosomes derived from RAW264.7 cells.
DOI: 10.25582/data.2023-01.2710900/2305138
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2709497/2305139
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.7075697
title: Transcriptome sequencing and expression profiling of genes involved in the response to abiotic stress in Medicago ruthenica

description: Abstract Medicago ruthenica is a perennial forage legume with the remarkable ability to survive under unfavorable environmental conditions. It has been identified as an excellent species of Medicago that can adapt to various environmental stresses including low temperature, drought, and salinity. To investigate its potential as a genetic resource, we performed transcriptome sequencing and analysis in M. ruthenica under abiotic stresses. We generated &gt;120 million reads from six cDNA libraries, resulting in 79,249 unique transcripts, most of which were highly similar to transcripts from M. truncatula (44,608, 56.3%) and alfalfa (M. sativa, 48,023, 60.6%). Based on gene expression profiles, 2,721 transcripts were identified as abiotic stress responsive genes which were predicted to be mainly involved in phytohormone signaling pathways, transcriptional regulation, and ROS-scavenging. These results suggest that they play critical roles in the response to abiotic stress. In summary, we identified genes in our transcriptome dataset involved in the regulation of the abiotic stress response in M. ruthenica which will provide a valuable resource for the future identification and functional analysis of candidate genes for adaption to unfavorable conditions. The genes identified here could be also useful for improving stress tolerance traits in alfalfa through molecular breeding in the future.
DOI: 10.6084/m9.figshare.7075697.v1
title: Transcriptome sequencing and expression profiling of genes involved in the response to abiotic stress in Medicago ruthenica

description: Abstract Medicago ruthenica is a perennial forage legume with the remarkable ability to survive under unfavorable environmental conditions. It has been identified as an excellent species of Medicago that can adapt to various environmental stresses including low temperature, drought, and salinity. To investigate its potential as a genetic resource, we performed transcriptome sequencing and analysis in M. ruthenica under abiotic stresses. We generated &gt;120 million reads from six cDNA libraries, resulting in 79,249 unique transcripts, most of which were highly similar to transcripts from M. truncatula (44,608, 56.3%) and alfalfa (M. sativa, 48,023, 60.6%). Based on gene expression profiles, 2,721 transcripts were identified as abiotic stress responsive genes which were predicted to be mainly involved in phytohormone signaling pathways, transcriptional regulation, and ROS-scavenging. These results suggest that they play critical roles in the response to abiotic stress. In summary, we identified genes in our transcriptome dataset involved in the regulation of the abiotic stress response in M. ruthenica which will provide a valuable resource for the future identification and functional analysis of candidate genes for adaption to unfavorable conditions. The genes identified here could be also useful for improving stress tolerance traits in alfalfa through molecular breeding in the future.
DOI: 10.25582/data.2023-01.2710033/2305140
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.7075700
title: A cytosolic class II small heat shock protein, PfHSP17.2, confers resistance to heat, cold, and salt stresses in transgenic Arabidopsis

description: Abstract We cloned and characterized the full-length coding sequence of a small heat shock (sHSP) gene, PfHSP17.2, from Primula forrestii leaves following heat stress treatment. Homology and phylogenetic analysis suggested that PfHSP17.2 is a cytosolic class II sHSP, which was further supported by the cytosolic localization of transient expression of PfHSP17.2 fused with green fluorescent protein reporter. Expression analysis showed that PfHSP17.2 was highly inducible by heat stress in almost all the vegetative and generative tissues and was expressed under salt, cold, and oxidative stress conditions as well. Moreover, the expression of PfHSP17.2 in P. forrestii was detected in certain developmental growth stages. Transgenic Arabidopsis thaliana constitutively expressing PfHSP17.2 displayed increased thermotolerance and higher resistance to salt and cold compared with wild type plants. It is suggested that PfHSP17.2 plays a key role in heat and other abiotic stresses.
DOI: 10.6084/m9.figshare.7075700.v1
title: A cytosolic class II small heat shock protein, PfHSP17.2, confers resistance to heat, cold, and salt stresses in transgenic Arabidopsis

description: Abstract We cloned and characterized the full-length coding sequence of a small heat shock (sHSP) gene, PfHSP17.2, from Primula forrestii leaves following heat stress treatment. Homology and phylogenetic analysis suggested that PfHSP17.2 is a cytosolic class II sHSP, which was further supported by the cytosolic localization of transient expression of PfHSP17.2 fused with green fluorescent protein reporter. Expression analysis showed that PfHSP17.2 was highly inducible by heat stress in almost all the vegetative and generative tissues and was expressed under salt, cold, and oxidative stress conditions as well. Moreover, the expression of PfHSP17.2 in P. forrestii was detected in certain developmental growth stages. Transgenic Arabidopsis thaliana constitutively expressing PfHSP17.2 displayed increased thermotolerance and higher resistance to salt and cold compared with wild type plants. It is suggested that PfHSP17.2 plays a key role in heat and other abiotic stresses.
DOI: 10.6084/m9.figshare.9697142
title: Involvement of TLR4 in the protective effect of intra-articular administration of curcumin on rat experimental osteoarthritis

description: Abstract Purpose In view of the principal role of Toll-like receptor 4 (TLR4) in mediating sterile inflammatory response contributing to osteoarthritis (OA) pathogenesis, we used lipopolysaccharide (LPS), a known TLR4 activator, to clarify whether modulation of TLR4 contributed to the protective actions of intra-articular administration of curcumin in a classical rat OA model surgically induced by anterior cruciate ligament transection (ACLT). Methods The rats underwent ACLT and received 50μl of curcumin at the concentration of 1 mg mL-1 and 10 μg LPS by intra-articular injection once a week for 8 weeks. Morphological changes of the cartilage and synovial tissues were observed. Apoptotic chondrocytes were detected using TUNEL assay. The concentrations of IL-1β and TNF-ɑ in synovial fluid were determined using ELISA kits. The mRNA and protein expression levels of TLR4 and NF-κB p65 were detected by real-time PCR and Western blotting, respectively. Results Intra-articular administration of curcumin significantly improved articular cartilage injury, suppressed synovial inflammation and down-regulated the overexpression of TLR4 and its downstream NF-κB caused by LPS-induced TLR4 activation in rat osteoarthritic knees. Conclusion The data suggested that the inhibition of TLR4 signal might be an important mechanism underlying a protective effect of local curcumin administration on OA.
DOI: 10.25582/data.2023-02.2732577/2305141
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.9697142.v1
title: Involvement of TLR4 in the protective effect of intra-articular administration of curcumin on rat experimental osteoarthritis

description: Abstract Purpose In view of the principal role of Toll-like receptor 4 (TLR4) in mediating sterile inflammatory response contributing to osteoarthritis (OA) pathogenesis, we used lipopolysaccharide (LPS), a known TLR4 activator, to clarify whether modulation of TLR4 contributed to the protective actions of intra-articular administration of curcumin in a classical rat OA model surgically induced by anterior cruciate ligament transection (ACLT). Methods The rats underwent ACLT and received 50μl of curcumin at the concentration of 1 mg mL-1 and 10 μg LPS by intra-articular injection once a week for 8 weeks. Morphological changes of the cartilage and synovial tissues were observed. Apoptotic chondrocytes were detected using TUNEL assay. The concentrations of IL-1β and TNF-ɑ in synovial fluid were determined using ELISA kits. The mRNA and protein expression levels of TLR4 and NF-κB p65 were detected by real-time PCR and Western blotting, respectively. Results Intra-articular administration of curcumin significantly improved articular cartilage injury, suppressed synovial inflammation and down-regulated the overexpression of TLR4 and its downstream NF-κB caused by LPS-induced TLR4 activation in rat osteoarthritic knees. Conclusion The data suggested that the inhibition of TLR4 signal might be an important mechanism underlying a protective effect of local curcumin administration on OA.
DOI: 10.25582/data.2023-01.2712377/2305142
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2732792/2305143
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2733244/2305144
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-02.2733145/2305145
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.8124308.v1
title: SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection

description: Influenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. Despite reports of DI particles present in seasonal influenza A H1N1 infections, their existence in human infections by the avian influenza A viruses, such as H7N9, has not been studied. Here we report the ubiquitous presence of DI-RNAs in nasopharyngeal aspirates of H7N9-infected patients. Single Molecule Real Time (SMRT) sequencing was first applied and long-read sequencing analysis showed that a variety of H7N9 DI-RNA species were present in the patient samples and human bronchial epithelial cells. In several abundantly expressed DI-RNA species, long overlapping sequences have been identified around at the breakpoint region and the other side of deleted region. Influenza DI-RNA is known as a defective viral RNA with single large internal deletion. Beneficial to the long-read property of SMRT sequencing, double and triple internal deletions were identified in half of the DI-RNA species. In addition, we examined the expression of DI-RNAs in mice infected with sublethal dose of H7N9 virus at different time points. Interestingly, DI-RNAs were abundantly expressed as early as day 2 post-infection. Taken together, we reveal the diversity and characteristics of DI-RNAs found in H7N9-infected patients, cells and animals. Further investigations on this overwhelming generation of DI-RNA may provide important insights into the understanding of H7N9 viral replication and pathogenesis.
DOI: 10.25582/data.2023-01.2710829/2305146
title: Data for EMSL Project 51287 from January 2023
DOI: 10.6084/m9.figshare.8124308.v2
title: SMRT sequencing revealed the diversity and characteristics of defective interfering RNAs in influenza A (H7N9) virus infection

description: Influenza defective interfering (DI) particles are replication-incompetent viruses carrying large internal deletion in the genome. The loss of essential genetic information causes abortive viral replication, which can be rescued by co-infection with a helper virus that possesses an intact genome. Despite reports of DI particles present in seasonal influenza A H1N1 infections, their existence in human infections by the avian influenza A viruses, such as H7N9, has not been studied. Here we report the ubiquitous presence of DI-RNAs in nasopharyngeal aspirates of H7N9-infected patients. Single Molecule Real Time (SMRT) sequencing was first applied and long-read sequencing analysis showed that a variety of H7N9 DI-RNA species were present in the patient samples and human bronchial epithelial cells. In several abundantly expressed DI-RNA species, long overlapping sequences have been identified around at the breakpoint region and the other side of deleted region. Influenza DI-RNA is known as a defective viral RNA with single large internal deletion. Beneficial to the long-read property of SMRT sequencing, double and triple internal deletions were identified in half of the DI-RNA species. In addition, we examined the expression of DI-RNAs in mice infected with sublethal dose of H7N9 virus at different time points. Interestingly, DI-RNAs were abundantly expressed as early as day 2 post-infection. Taken together, we reveal the diversity and characteristics of DI-RNAs found in H7N9-infected patients, cells and animals. Further investigations on this overwhelming generation of DI-RNA may provide important insights into the understanding of H7N9 viral replication and pathogenesis.
DOI: 10.25582/data.2023-01.2705732/2305147
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2733191/2305148
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2705470/2305149
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2733155/2305150
title: Data for EMSL Project 51287 from February 2023
DOI: 10.25582/data.2023-01.2705986/2305151
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2706047/2305152
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-01.2710560/2305153
title: Data for EMSL Project 51287 from January 2023
DOI: 10.25582/data.2023-02.2733255/2305154
title: Data for EMSL Project 51287 from February 2023
DOI: 10.6084/m9.figshare.17037210
title: Additional file 10 of The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

description: Table S10. The sentences with PPIs and proteins’ role & state information extracted from “BioCreAtIvE PPI” corpus by the PPIO-based method.
DOI: 10.6084/m9.figshare.17037210.v1
title: Additional file 10 of The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

description: Table S10. The sentences with PPIs and proteins’ role & state information extracted from “BioCreAtIvE PPI” corpus by the PPIO-based method.
DOI: 10.6084/m9.figshare.17037216
title: Additional file 11 of The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

description: Table S11. The sentences with PPIs and detection method information extracted from “BioCreAtIvE PPI” corpus by the PPIO-based method.
DOI: 10.6084/m9.figshare.17037216.v1
title: Additional file 11 of The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction

description: Table S11. The sentences with PPIs and detection method information extracted from “BioCreAtIvE PPI” corpus by the PPIO-based method.