cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccdc.csd.cc2fn64g
title: CCDC 2253735: Experimental Crystal Structure Determination

description: Related Article: Subhash Bairagi, Soumen Giri, Deepak Kumar Patel, Diana Luong, Boniface P. T. Fokwa, Sundargopal Ghosh|2024|Dalton Trans.|53|3191|doi:10.1039/D3DT03907B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2fvsz2
title: CCDC 2260085: Experimental Crystal Structure Determination

description: Related Article: Nalin Abeydeera, Khalil Mudarmah, Bishnu D. Pant, Jeanette A. Krause, Yao-Rong Zheng, Songping D. Huang|2024|Dalton Trans.|53|3206|doi:10.1039/D3DT02517A
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g0rdn
title: CCDC 2264841: Experimental Crystal Structure Determination

description: Related Article: Ming-Hui Liu, Wei-Yang Wen, Hong-Yao Shen, Yan Yang, Jun Li, Bo Zhang|2024|Dalton Trans.|53|2991|doi:10.1039/D3DT03264G
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2g318x
title: CCDC 2267038: Experimental Crystal Structure Determination

description: Related Article: Ju-Ju Liang, Yu-Chun Lin, Zhi-Han Chang, Xiuli Wang|2024|Dalton Trans.|53|3020|doi:10.1039/D3DT04195F
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.22735590.v1
title: Additional file 6 of H3K4me3-related lncRNAs signature and comprehensive analysis of H3K4me3 regulating tumor immunity in lung adenocarcinoma

description: Supplementary Material 6
DOI: 10.5517/ccdc.csd.cc2ggy96
title: CCDC 2278478: Experimental Crystal Structure Determination

description: Related Article: Marina Yu. Stogniy, Sergey A. Anufriev, Ekaterina V. Bogdanova, Nadezhda A. Gorodetskaya, Alexei A. Anisimov, Kyrill Yu. Suponitsky, Ivan D. Grishin, Igor B. Sivaev|2024|Dalton Trans.|53|3363|doi:10.1039/D3DT03549B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.7531253
title: PAX3-FOXO1 escapes miR-495 regulation during muscle differentiation

description: Pax3 plays an essential role in myogenesis. Previously, we found a tumor-signature chimeric fusion RNA, <i>PAX3-FOXO1</i> also present during muscle differentiation, raising the possibility of its physiological role. Here we demonstrated that the fusion is needed transiently for muscle lineage commitment. Interestingly, the fusion ortholog was not found in seven mouse muscle differentiation/regeneration systems, nor in other stem cell differentiation systems of another three mammal species. We noticed that <i>Pax3</i> is expressed at a much lower level in human stem cells, and during muscle differentiation than in other mammals. Given the fact that the fusion and the parental Pax3 share common downstream targets, we reasoned that forming the fusion may be a mechanism for human cells to escape certain microRNA regulation on <i>Pax3</i>. By sequence comparison, we identified 16 candidate microRNAs that may specifically target the human <i>PAX3</i> 3ʹUTR. We used a luciferase reporter assay, examined the microRNAs expression, and conducted mutagenesis on the reporters, as well as a CRISPR/Cas9 mediated editing on the endogenous allele. Finally, we identified miR-495 as a microRNA that specifically targets human <i>PAX3</i>. Examining several other fusion RNAs revealed that the human-specificity is not limited to <i>PAX3-FOXO1</i>. Based on these observations, we conclude that <i>PAX3-FOXO1</i> fusion RNA is absent in mouse, or other mammals we tested, the fusion RNA is a mechanism to escape microRNA, miR-495 regulation in humans, and that it is not the only human-specific fusion RNA.
DOI: 10.5517/ccdc.csd.cc2ggyb7
title: CCDC 2278479: Experimental Crystal Structure Determination

description: Related Article: Marina Yu. Stogniy, Sergey A. Anufriev, Ekaterina V. Bogdanova, Nadezhda A. Gorodetskaya, Alexei A. Anisimov, Kyrill Yu. Suponitsky, Ivan D. Grishin, Igor B. Sivaev|2024|Dalton Trans.|53|3363|doi:10.1039/D3DT03549B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ggyc8
title: CCDC 2278480: Experimental Crystal Structure Determination

description: Related Article: Marina Yu. Stogniy, Sergey A. Anufriev, Ekaterina V. Bogdanova, Nadezhda A. Gorodetskaya, Alexei A. Anisimov, Kyrill Yu. Suponitsky, Ivan D. Grishin, Igor B. Sivaev|2024|Dalton Trans.|53|3363|doi:10.1039/D3DT03549B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2ggyd9
title: CCDC 2278481: Experimental Crystal Structure Determination

description: Related Article: Marina Yu. Stogniy, Sergey A. Anufriev, Ekaterina V. Bogdanova, Nadezhda A. Gorodetskaya, Alexei A. Anisimov, Kyrill Yu. Suponitsky, Ivan D. Grishin, Igor B. Sivaev|2024|Dalton Trans.|53|3363|doi:10.1039/D3DT03549B
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.6084/m9.figshare.21162883
title: Additional file 1 of The extremely reduced, diverged and reconfigured plastomes of the largest mycoheterotrophic orchid lineage

description: Additional file 1.
DOI: 10.6084/m9.figshare.7007228
title: Genome-wide profiling of sRNAs in the <i>Verticillium dahliae</i>-infected <i>Arabidopsis</i> roots

description: Small RNAs (sRNAs, including small interfering RNAs [siRNAs] and micro RNAs [miRNAs]) are key mediators of RNA silencing (or RNA interference), which play important roles in plant development and response to biotic and abiotic stimulation. Verticillium wilt is a plant vascular disease caused by the soil-borne fungal pathogens, such as <i>Verticillium dahliae</i>. We previously reported that <i>V. dahliae</i> infection increased two plant endogenous miRNAs that were exported to fungal cell to silence virulence genes. To investigate plant sRNAs in genome-wide response to <i>V. dahliae</i> infection, in this study, we constructed two sRNA libraries from <i>Arabidopsis</i> roots with and without <i>V. dahliae</i> infection, respectively. In total, 31 conserved miRNAs were found to be differentially expressed during the early stage of infection with <i>V. dahliae</i> using sRNA sequencing. Among these, the expression levels of miR160, miR164, miR166, miR167, miR390 and miR156h were confirmed by northern blot. Reverse transcription quantitative real time polymerase chain reaction results showed that the induction of miRNAs (miR160, miR164, miR166 and miR167) upon <i>V. dahliae</i> infection downregulated the expression of their targeted genes (<i>ARF10, NAC1, PHV</i> and <i>ARF6</i>), respectively. In addition, we identified specific phased siRNAs generated from distinct regions of two libraries. Profiling of these miRNAs and sRNAs lay the foundation for further understanding and utilising the host-induced gene silencing strategy to control plant vascular pathogens.
DOI: 10.6084/m9.figshare.21687319.v1
title: High expression of COL6A1 predicts poor prognosis and response to immunotherapy in bladder cancer

description: Extracellular matrix (ECM), as an important framework for tumor microenvironment, plays important roles in many critical processes, including tumor growth, invasion, immune suppression, and drug resistance. However, few biomarkers of ECM-related genes (ERGs) have been developed for prognosis prediction and clinical treatment of bladder cancer (BC) patients. Bioinformatics analysis and LC-MS/MS analysis were used to screen differentially expressed ERGs in BC. Multivariate Cox regression analysis and Lasso regression analysis were used to construct and validate an ERGs-based prognostic prediction model for BC. Immunohistochemistry was used to detect the protein expression of hub gene-COL6A1 in BC patients. Using bioinformatics analysis from The Cancer Genome Atlas (TCGA) database and proteomic analysis from our BC cohort, we constructed and validated an effective prognostic prediction model for BC patients based on four differentially expressed ERGs (MAP1B, FBN1, COL6A1, and MFAP5). Moreover, we identified human collagen VI-COL6A1 was a hub gene in this prognostic prediction model and found that COL6A1 was closely related to malignancy progression, prognosis, and response to PD-1 inhibitor immunotherapy in BC. Our findings highlight the satisfactory predictive value of ECM-related prognostic models in BC and suggested that COL6A1 may be a potential biomarker in predicting malignant progression, prognosis, and efficacy of immunotherapy in BC.
DOI: 10.6084/m9.figshare.22211639.v1
title: Mapping Resident Immune Cells in the Murine Ocular Surface and Lacrimal Gland by Flow Cytometry

description: The ocular surface and lacrimal gland have a frontline position in mucosal immunology. However, there have been few updates to the immune cell atlas of these tissues in recent years. To map the immune cells in murine ocular surface tissues and lacrimal gland. Central and peripheral corneas, conjunctiva, and lacrimal gland were dissociated into single cell suspensions, followed by flow cytometry. Discrepancy of immune cells between the central and peripheral corneas was compared. In the conjunctiva and lacrimal gland, myeloid cells were clustered by tSNE and FlowSOM based on the expression of F4/80, Ly6C, Ly6G, and MHC II. ILCs, type 1 immune cells, and type 3 immune cells were analyzed. The number of immune cells in peripheral corneas was about 16 folds of that in central corneas. B cells accounted for 8.74% of immune cells in murine peripheral corneas. In the conjunctiva and lacrimal gland, most myeloid cells tended out to be monocytes, macrophages, and classical dendritic cells (cDCs). ILC3 were 6.28% and 3.63% of ILCs in the conjunctiva and lacrimal gland, respectively. Th1, Tc1, and NK cells were predominant type 1 immune cells. γδ T17 cells and ILC3 outnumbered Th17 cells among type 3 T cells. B cells resident in murine corneas were reported for the first time. Additionally, we proposed a strategy of clustering myeloid cells to better understand their heterogeneity in the conjunctiva and lacrimal gland based on tSNE and FlowSOM. Furthermore, we identified the ILC3 in the conjunctiva and lacrimal gland for the first time. Compositions of type 1 and type 3 immune cells were summarized. Our study provides a fundamental reference and novel insights for ocular surface immune homeostasis and diseases.
DOI: 10.6084/m9.figshare.21162883.v1
title: Additional file 1 of The extremely reduced, diverged and reconfigured plastomes of the largest mycoheterotrophic orchid lineage

description: Additional file 1.
DOI: 10.6084/m9.figshare.19581990
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.21162781
title: Additional file 1 of Effects of nursing support workers participation on negative emotions, quality of life and life satisfaction of patients with cerebral hemorrhage: a quasi-experimental study

description: Additional file 1.
DOI: 10.6084/m9.figshare.19581954
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: 10.6084/m9.figshare.19581984
title: Additional file 7 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 7. 12864_2022_8515_MOESM7_ESM.xlsx.
DOI: 10.6084/m9.figshare.7531808.v1
title: Additional file 1: of miR-18a reactivates the Epstein-Barr virus through defective DNA damage response and promotes genomic instability in EBV-associated lymphomas

description: Figure S1. Visualization of episomal and integrated EBV DNA by fluorescence in situ hybridization in EBV-positive or -negative BJAB cells. Figure S2. EBV infection increased the expression of miR-18a. Real-time PCR was used to measure the mRNA expression of EBV-related genes. Figure S3. Expression of ATM as measured by western blotting after transfection of miR-18a in EBV-negative BJAB. cells. (ZIP 3643 kb)
DOI: 10.6084/m9.figshare.23260145.v1
title: A real-world data analysis of topotecan in the FDA Adverse Event Reporting System (FAERS) database

description: The objective of this study was to monitor and identify adverse events (AEs) associated with topotecan, a medication used for the treatment of solid tumors, in order to improve patient safety and guide medication usage. To assess the disproportionality of topotecan-related AEs in real-world data, four algorithms (ROR, PRR, BCPNN, and EBGM) were employed as measures to detect signals of topotecan-associated AEs. A statistical analysis was conducted using data from the FAERS database, encompassing 9,511,161 case reports from 2004Q1 to 2021Q4. Among these reports, 1,896 were identified as primary suspected (PS) AEs related to topotecan, and 155 topotecan-related adverse drug reactions (ADRs) at the preferred terms (PTs) level were selected. The occurrence of topotecan-induced ADRs was analyzed across 23 organ systems. The analysis revealed several expected ADRs, such as anemia, nausea, and vomiting, which were consistent with the drug labels. Additionally, unexpected significant ADRs associated with eye disorders at the system organ class (SOC) level were identified, indicating potential adverse effects not currently mentioned in the drug instructions. This study identified new and unexpected signals of adverse drug reactions (ADRs) related to topotecan, providing valuable insights into the relationship between ADRs and topotecan usage. The findings highlight the importance of ongoing monitoring and surveillance to detect and manage AEs effectively, ultimately improving patient safety during topotecan treatment.
DOI: 10.6084/m9.figshare.19581987
title: Additional file 8 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 8. 12864_2022_8515_MOESM8_ESM.xlsx.
DOI: 10.6084/m9.figshare.13298688.v1
title: Additional file 4 of Genomic patterns and characterizations of chromosomally-encoded mcr-1 in Escherichia coli populations

description: Additional file 4: Appendix.
DOI: 10.6084/m9.figshare.13298688
title: Additional file 4 of Genomic patterns and characterizations of chromosomally-encoded mcr-1 in Escherichia coli populations

description: Additional file 4: Appendix.
DOI: 10.6084/m9.figshare.21687319
title: High expression of COL6A1 predicts poor prognosis and response to immunotherapy in bladder cancer

description: Extracellular matrix (ECM), as an important framework for tumor microenvironment, plays important roles in many critical processes, including tumor growth, invasion, immune suppression, and drug resistance. However, few biomarkers of ECM-related genes (ERGs) have been developed for prognosis prediction and clinical treatment of bladder cancer (BC) patients. Bioinformatics analysis and LC-MS/MS analysis were used to screen differentially expressed ERGs in BC. Multivariate Cox regression analysis and Lasso regression analysis were used to construct and validate an ERGs-based prognostic prediction model for BC. Immunohistochemistry was used to detect the protein expression of hub gene-COL6A1 in BC patients. Using bioinformatics analysis from The Cancer Genome Atlas (TCGA) database and proteomic analysis from our BC cohort, we constructed and validated an effective prognostic prediction model for BC patients based on four differentially expressed ERGs (MAP1B, FBN1, COL6A1, and MFAP5). Moreover, we identified human collagen VI-COL6A1 was a hub gene in this prognostic prediction model and found that COL6A1 was closely related to malignancy progression, prognosis, and response to PD-1 inhibitor immunotherapy in BC. Our findings highlight the satisfactory predictive value of ECM-related prognostic models in BC and suggested that COL6A1 may be a potential biomarker in predicting malignant progression, prognosis, and efficacy of immunotherapy in BC.
DOI: 10.6084/m9.figshare.12774832.v1
title: Additional file 1 of Comprehensive identification and analysis of DELLA genes throughout the plant kingdom

description: Additional file 1: Table S1. Amino acid sequences of DELLAs in various species. Information includes the species name, gene name, amino acid sequence, and domain composition.
DOI: 10.6084/m9.figshare.12774832
title: Additional file 1 of Comprehensive identification and analysis of DELLA genes throughout the plant kingdom

description: Additional file 1: Table S1. Amino acid sequences of DELLAs in various species. Information includes the species name, gene name, amino acid sequence, and domain composition.
DOI: 10.6084/m9.figshare.22211639
title: Mapping Resident Immune Cells in the Murine Ocular Surface and Lacrimal Gland by Flow Cytometry

description: The ocular surface and lacrimal gland have a frontline position in mucosal immunology. However, there have been few updates to the immune cell atlas of these tissues in recent years. To map the immune cells in murine ocular surface tissues and lacrimal gland. Central and peripheral corneas, conjunctiva, and lacrimal gland were dissociated into single cell suspensions, followed by flow cytometry. Discrepancy of immune cells between the central and peripheral corneas was compared. In the conjunctiva and lacrimal gland, myeloid cells were clustered by tSNE and FlowSOM based on the expression of F4/80, Ly6C, Ly6G, and MHC II. ILCs, type 1 immune cells, and type 3 immune cells were analyzed. The number of immune cells in peripheral corneas was about 16 folds of that in central corneas. B cells accounted for 8.74% of immune cells in murine peripheral corneas. In the conjunctiva and lacrimal gland, most myeloid cells tended out to be monocytes, macrophages, and classical dendritic cells (cDCs). ILC3 were 6.28% and 3.63% of ILCs in the conjunctiva and lacrimal gland, respectively. Th1, Tc1, and NK cells were predominant type 1 immune cells. γδ T17 cells and ILC3 outnumbered Th17 cells among type 3 T cells. B cells resident in murine corneas were reported for the first time. Additionally, we proposed a strategy of clustering myeloid cells to better understand their heterogeneity in the conjunctiva and lacrimal gland based on tSNE and FlowSOM. Furthermore, we identified the ILC3 in the conjunctiva and lacrimal gland for the first time. Compositions of type 1 and type 3 immune cells were summarized. Our study provides a fundamental reference and novel insights for ocular surface immune homeostasis and diseases.
DOI: 10.6084/m9.figshare.23260145
title: A real-world data analysis of topotecan in the FDA Adverse Event Reporting System (FAERS) database

description: The objective of this study was to monitor and identify adverse events (AEs) associated with topotecan, a medication used for the treatment of solid tumors, in order to improve patient safety and guide medication usage. To assess the disproportionality of topotecan-related AEs in real-world data, four algorithms (ROR, PRR, BCPNN, and EBGM) were employed as measures to detect signals of topotecan-associated AEs. A statistical analysis was conducted using data from the FAERS database, encompassing 9,511,161 case reports from 2004Q1 to 2021Q4. Among these reports, 1,896 were identified as primary suspected (PS) AEs related to topotecan, and 155 topotecan-related adverse drug reactions (ADRs) at the preferred terms (PTs) level were selected. The occurrence of topotecan-induced ADRs was analyzed across 23 organ systems. The analysis revealed several expected ADRs, such as anemia, nausea, and vomiting, which were consistent with the drug labels. Additionally, unexpected significant ADRs associated with eye disorders at the system organ class (SOC) level were identified, indicating potential adverse effects not currently mentioned in the drug instructions. This study identified new and unexpected signals of adverse drug reactions (ADRs) related to topotecan, providing valuable insights into the relationship between ADRs and topotecan usage. The findings highlight the importance of ongoing monitoring and surveillance to detect and manage AEs effectively, ultimately improving patient safety during topotecan treatment.
DOI: 10.6084/m9.figshare.7531808
title: Additional file 1: of miR-18a reactivates the Epstein-Barr virus through defective DNA damage response and promotes genomic instability in EBV-associated lymphomas

description: Figure S1. Visualization of episomal and integrated EBV DNA by fluorescence in situ hybridization in EBV-positive or -negative BJAB cells. Figure S2. EBV infection increased the expression of miR-18a. Real-time PCR was used to measure the mRNA expression of EBV-related genes. Figure S3. Expression of ATM as measured by western blotting after transfection of miR-18a in EBV-negative BJAB. cells. (ZIP 3643 kb)
DOI: 10.6084/m9.figshare.19581957.v1
title: Additional file 11 of Identification of circRNA-associated ceRNA networks using longissimus thoracis of pigs of different breeds and growth stages

description: Additional file 11. 12864_2022_8515_MOESM11_ESM.xlsx.
DOI: 10.13145/bacdive9997.20170829.2
title: Myxococcus xanthus Beebe 1941

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.
DOI: 10.13145/bacdive9998.20170829.2
title: Myxococcus xanthus Beebe 1941

description: The range of data encompasses taxonomy, morphology, physiology, sampling and concomitant environmental conditions as well as molecular biology.