cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19808484
title: Healthy humans can be a source of antibodies countering COVID-19

description: Here, we describe the isolation of 18 unique anti SARS-CoV-2 human single-chain antibodies from an antibody library derived from healthy donors. The selection used a combination of phage and yeast display technologies and included counter-selection strategies meant to direct the selection of the receptor-binding motif (RBM) of SARS-CoV-2 spike protein’s receptor binding domain (RBD2). Selected antibodies were characterized in various formats including IgG, using flow cytometry, ELISA, high throughput SPR, and fluorescence microscopy. We report antibodies’ RBD2 recognition specificity, binding affinity, and epitope diversity, as well as ability to block RBD2 binding to the human receptor angiotensin-converting enzyme 2 (ACE2) and to neutralize authentic SARS-CoV-2 virus infection in vitro. We present evidence supporting that: 1) most of our antibodies (16 out of 18) selectively recognize RBD2; 2) the best performing 8 antibodies target eight different epitopes of RBD2; 3) one of the pairs tested in sandwich assays detects RBD2 with sub-picomolar sensitivity; and 4) two antibody pairs inhibit SARS-CoV-2 infection at low nanomolar half neutralization titers. Based on these results, we conclude that our antibodies have high potential for therapeutic and diagnostic applications. Importantly, our results indicate that readily available non immune (naïve) antibody libraries obtained from healthy donors can be used to select high-quality monoclonal antibodies, bypassing the need for blood of infected patients, and offering a widely accessible and low-cost alternative to more sophisticated and expensive antibody selection approaches (e.g. single B cell analysis and natural evolution in humanized mice).
DOI: 10.6084/m9.figshare.19808167
title: Additional file 7 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 7: Table S6. KEGG enrich for BT45vsAT37.
DOI: 10.6084/m9.figshare.19808463.v1
title: Circadian Period 2 (Per2) downregulate inhibitor of differentiation 3 (Id3) expression via PTEN/AKT/Smad5 axis to inhibits glioma cell proliferation

description: In this study, we employed multiple laboratory techniques to acknowledge the biological activities and processes of Per2 and Id3 in glioma. We analyzed TCGA and CGGA databases for seeking association among Per2, Id3, and clinical features in glioma. Immunohistochemistry and Western blot were used to detect protein expression levels. CCK-8 assay, colony formation assay, Transwell assay, the wound healing assay, flow cytometric, and Xenograft nude mice were used to acknowledge the impact of Per2 and Id3 on biological behavior of glioma. The results showed that the Per2 mRNA expression was negatively correlated with the WHO grade, while the Id3 mRNA expression was positively correlated with the WHO grade in patients with glioma in TCGA and CGGA databases. Per2 and Id3 maintained separate prognostic abilities and had a negative connection in human glioma. In the clinical sample study, Per2 and Id3 were validated at the protein level with the same results compared to the mRNA expression level in TCGA and CGGA. By using a wide range of functional examples, overexpression of Per2 restrains malignant biological behaviors in glioma cells by many ways, while Id3 promotes malignant biological behaviors in glioma cells. Furthermore, overexpression of Per2 can inhibit Id3 expression via regulating PTEN/AKT/Smad5 signaling pathway and thereby abolish malignant biological behaviors that are caused by Id3 overexpression. These results suggested that Per2 inhibits glioma cell proliferation through regulating PTEN/AKT/Smad5/Id3 signaling pathway, which may be a viable therapeutic target for glioma.
DOI: 10.6084/m9.figshare.19808485
title: Long non-coding RNA H19 alleviates hippocampal damage in convulsive status epilepticus rats through the nuclear factor-kappaB signaling pathway

description: Previous studies have demonstrated that inflammation plays a critical role in hippocampcal damage and cognitive dysfunction induced by convulsive status epilepticus (CSE). Emerging evidence indicated that the long non-coding RNA (lncRNA) H19 acts as an important regulator of inflammation in various diseases. However, the role of H19 in CSE is still unkonwn. In the present study, pilocarpine-induced SE rat model was used to explore the role of H19 in hippocampal neuron damage in CSE. Our results indicated that the increased level of H19 is positively correlated with the expression of inflammatory cytokines (TNF-α and IL-1β) in hippocampus of SE rats. Moreover, knockdown of H19 could inhibit the activation of microglia and suppress the expression of inflammatory cytokines via nuclear factor-kappaB (NF-κB) signaling pathway. It was further revealed that downregulation of H19 could alleviate hippocampal neuron damage induced by CSE. These findings indicated that H19 modulates inflammatory response and hippocampal damage through the NF-κB signaling pathway in the CSE rats, which provides a promising target to alleviate hippocampcal damage of CSE.
DOI: 10.6084/m9.figshare.19808146
title: Additional file 15 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 15: Table S14. Information of correlation analysis by multiple omics.
DOI: 10.6084/m9.figshare.19808484.v1
title: Healthy humans can be a source of antibodies countering COVID-19

description: Here, we describe the isolation of 18 unique anti SARS-CoV-2 human single-chain antibodies from an antibody library derived from healthy donors. The selection used a combination of phage and yeast display technologies and included counter-selection strategies meant to direct the selection of the receptor-binding motif (RBM) of SARS-CoV-2 spike protein’s receptor binding domain (RBD2). Selected antibodies were characterized in various formats including IgG, using flow cytometry, ELISA, high throughput SPR, and fluorescence microscopy. We report antibodies’ RBD2 recognition specificity, binding affinity, and epitope diversity, as well as ability to block RBD2 binding to the human receptor angiotensin-converting enzyme 2 (ACE2) and to neutralize authentic SARS-CoV-2 virus infection in vitro. We present evidence supporting that: 1) most of our antibodies (16 out of 18) selectively recognize RBD2; 2) the best performing 8 antibodies target eight different epitopes of RBD2; 3) one of the pairs tested in sandwich assays detects RBD2 with sub-picomolar sensitivity; and 4) two antibody pairs inhibit SARS-CoV-2 infection at low nanomolar half neutralization titers. Based on these results, we conclude that our antibodies have high potential for therapeutic and diagnostic applications. Importantly, our results indicate that readily available non immune (naïve) antibody libraries obtained from healthy donors can be used to select high-quality monoclonal antibodies, bypassing the need for blood of infected patients, and offering a widely accessible and low-cost alternative to more sophisticated and expensive antibody selection approaches (e.g. single B cell analysis and natural evolution in humanized mice).
DOI: 10.6084/m9.figshare.19808482.v1
title: CircNMD3 relieves endothelial cell injury induced by oxidatively modified low-density lipoprotein through regulating miR-498/ BMP and activin membrane-bound inhibitor (BAMBI) axis

description: Atherosclerosis (AS) is one of the most common vascular diseases. The endothelial injury theory indicates that atherosclerotic plaque is the result of endothelial cell injury. Recent studies have revealed that circRNAs are abnormally expressed in AS cell models, which are implicated in the regulation of various cell behaviors. In this study, we showed the downregulation of circNMD3 in AS, and studied its role in the model of endothelial cell injury by proliferation and apoptosis assay, caspase 3 activity assay, and ELISA. We also identified and validated its downstream targets by luciferase reporter assay, RNA pull-down experiment, Western blot, and RT-qPCR. CircNMD3 overexpression or miR-498 knockdown could inhibit the ox-LDL (oxidatively modified low-density lipoprotein)-induced injury in HUVEC (human umbilical vein endothelial cells), while the co-transfection of miR-498 mimic or siRNA targeting BAMBI (BMP and activin membrane bound inhibitor) attenuated the protective effect of circNMD3 overexpression. Overall, our data suggest that circNMD3 regulates the miR-498/BAMBI axis in endothelial cells to protect ox-LDL-induced damages. As a molecular sponge of miR-498, circNMD3 regulates the level of miR-498, which in turn modulates BAMBI expression and suppresses ox-LDL-induced injury in HUVECs.
DOI: 10.6084/m9.figshare.8798483
title: Chemostratigraphy of the Lower Cretaceous dinosaur-bearing Xiagou and Zhonggou formations, Yujingzi Basin, northwest China

description: The Early Cretaceous of northwest China has yielded abundant vertebrates, invertebrates, and plant fossils from numerous intermontane basins. Developing a chronostratigraphic context for these important fossil finds is important to understanding the development of modern terrestrial ecosystems, the evolution of dinosaurs, and the Cretaceous greenhouse climate. This study utilizes carbon isotope chemostratigraphy of the fossil-rich Xinminpu Group in the Yujingzi Basin in northwest Gansu Province. Lithostratigraphic descriptions defined three facies. The lowest is a tan, coarse arkosic sandstone, overlain by gray to variegated mudstones, sandstones, and thin limestones, which transition to red sandstones, conglomerates, and mudstones. Depositional environment interpretation of these lithofacies assisted in refining 450 samples of bulk sedimentary organic carbon as well as charcoal samples to develop a composite curve to correlate to existing carbon isotope curves from the region and to better constrained Cretaceous sections globally. The carbon isotope curve is correlated based on the broad positive excursion associated with carbon isotope fluctuations of the Paquier Episode that spans the late Aptian to early Albian. Based on this correlation, the middle gray mudstone facies, which contains a diverse fauna including theropods, sauropods, and ornithopods, as well as turtles and invertebrates, is placed within the upper Aptian. The upper red sandstone facies, which contains therizinosaurs and the ceratopsian dinosaur <i>Auroraceratops</i>, is placed in the lower Albian. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Suarez, M. B., T. Milder, P. Nan, C. A. Suarez, H. You, D. Li, and P. Dodson 2019. Chemostratigraphy of the Lower Cretaceous dinosaur-bearing Xiagou and Zhonggou formations, Yujingzi Basin, northwest China; pp. 12–21 in Hailu You, Peter Dodson, and Eric Morschhauser (eds.), <i>Auroraceratops rugosus</i> (Ornithischia, Ceratopsia) from the Early Cretaceous of northwestern Gansu Province, China. Society of Vertebrate Paleontology Memoir 18. Journal of Vertebrate Paleontology 38(Supplement). DOI: 10.1080/02724634.2017.1510412.
DOI: 10.6084/m9.figshare.19808158.v1
title: Additional file 4 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 4: Table S3. GO enrich for BT45vsAT37.
DOI: 10.6084/m9.figshare.15089942
title: A ferroptosis-related gene signature for graft loss prediction following renal allograft

description: Allogeneic kidney transplantation (renal allograft) is the most effective treatment for advanced kidney disease. Previous studies have indicated that ferroptosis participates in the progression of acute kidney injury and renal transplant failure. However, few studies have evaluated the prognostic value of ferroptosis on renal transplantation outcomes. In this study, a total of 22 differentially expressed ferroptosis-related genes (DFGs) were identified, which were mainly enriched in infection-related pathways. Next, a ferroptosis-related gene signature, including GA-binding protein transcription factor subunit beta 1 (GABPB1), cyclin-dependent kinase inhibitor 1A (CDKN1A), Toll-like receptor 4 (TLR4), C-X-C motif chemokine ligand 2 (CXCL2), caveolin 1 (CAV1), and ribonucleotide reductase subunit M2 (RRM2), was constructed to predict graft loss following renal allograft. Moreover, receiver operating characteristic (ROC) curves (area under the ROC curve [AUC] &gt; 0.8) demonstrated the accuracy of the gene signature and univariate Cox analysis suggested that the gene signature could play an independent role in graft loss (p &lt; 0.05). Furthermore, the nomogram and calibration plots also indicated the good prognostic capability of the gene signature. Finally, immune-related and cytokine signaling pathways were mostly enriched in renal allograft patients with poor outcomes. Considered together, a ferroptosis-related gene signature and nomogram based on DFGs were created to predict the 1-, 2- and 3- year graft loss probability of renal allograft patients.The gene signature could serve as a valuable biomarker for predicting graft loss, contributing to improving the outcome of allogeneic kidney transplantation.
DOI: 10.6084/m9.figshare.8798483.v1
title: Chemostratigraphy of the Lower Cretaceous dinosaur-bearing Xiagou and Zhonggou formations, Yujingzi Basin, northwest China

description: The Early Cretaceous of northwest China has yielded abundant vertebrates, invertebrates, and plant fossils from numerous intermontane basins. Developing a chronostratigraphic context for these important fossil finds is important to understanding the development of modern terrestrial ecosystems, the evolution of dinosaurs, and the Cretaceous greenhouse climate. This study utilizes carbon isotope chemostratigraphy of the fossil-rich Xinminpu Group in the Yujingzi Basin in northwest Gansu Province. Lithostratigraphic descriptions defined three facies. The lowest is a tan, coarse arkosic sandstone, overlain by gray to variegated mudstones, sandstones, and thin limestones, which transition to red sandstones, conglomerates, and mudstones. Depositional environment interpretation of these lithofacies assisted in refining 450 samples of bulk sedimentary organic carbon as well as charcoal samples to develop a composite curve to correlate to existing carbon isotope curves from the region and to better constrained Cretaceous sections globally. The carbon isotope curve is correlated based on the broad positive excursion associated with carbon isotope fluctuations of the Paquier Episode that spans the late Aptian to early Albian. Based on this correlation, the middle gray mudstone facies, which contains a diverse fauna including theropods, sauropods, and ornithopods, as well as turtles and invertebrates, is placed within the upper Aptian. The upper red sandstone facies, which contains therizinosaurs and the ceratopsian dinosaur <i>Auroraceratops</i>, is placed in the lower Albian. SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at www.tandfonline.com/UJVP Citation for this article: Suarez, M. B., T. Milder, P. Nan, C. A. Suarez, H. You, D. Li, and P. Dodson 2019. Chemostratigraphy of the Lower Cretaceous dinosaur-bearing Xiagou and Zhonggou formations, Yujingzi Basin, northwest China; pp. 12–21 in Hailu You, Peter Dodson, and Eric Morschhauser (eds.), <i>Auroraceratops rugosus</i> (Ornithischia, Ceratopsia) from the Early Cretaceous of northwestern Gansu Province, China. Society of Vertebrate Paleontology Memoir 18. Journal of Vertebrate Paleontology 38(Supplement). DOI: 10.1080/02724634.2017.1510412.
DOI: 10.6084/m9.figshare.19808485.v1
title: Long non-coding RNA H19 alleviates hippocampal damage in convulsive status epilepticus rats through the nuclear factor-kappaB signaling pathway

description: Previous studies have demonstrated that inflammation plays a critical role in hippocampcal damage and cognitive dysfunction induced by convulsive status epilepticus (CSE). Emerging evidence indicated that the long non-coding RNA (lncRNA) H19 acts as an important regulator of inflammation in various diseases. However, the role of H19 in CSE is still unkonwn. In the present study, pilocarpine-induced SE rat model was used to explore the role of H19 in hippocampal neuron damage in CSE. Our results indicated that the increased level of H19 is positively correlated with the expression of inflammatory cytokines (TNF-α and IL-1β) in hippocampus of SE rats. Moreover, knockdown of H19 could inhibit the activation of microglia and suppress the expression of inflammatory cytokines via nuclear factor-kappaB (NF-κB) signaling pathway. It was further revealed that downregulation of H19 could alleviate hippocampal neuron damage induced by CSE. These findings indicated that H19 modulates inflammatory response and hippocampal damage through the NF-κB signaling pathway in the CSE rats, which provides a promising target to alleviate hippocampcal damage of CSE.
DOI: 10.6084/m9.figshare.19808134.v1
title: Additional file 11 of Multi-omics analyses of the mechanism for the formation of soy sauce-like and soybean flavor in Bacillus subtilis BJ3-2

description: Additional file 11: Table S10. GO annotation enrichment analysis in BP45_vs_AP37.
DOI: 10.6084/m9.figshare.19808122.v1
title: Additional file 3 of HCMV-miR-US33-5p promotes apoptosis of aortic vascular smooth muscle cells by targeting EPAS1/SLC3A2 pathway

description: Additional file 3: Table S2. Downregulated genes in HA-VSMCs transfected with HCMV-miR-US33-5p mimics.
DOI: 10.5281/zenodo.10696741
title: REMO-OASIS-MPIOM
DOI: 10.5281/zenodo.10696742
title: REMO-OASIS-MPIOM
DOI: 10.6084/m9.figshare.19808119.v1
title: Additional file 2 of HCMV-miR-US33-5p promotes apoptosis of aortic vascular smooth muscle cells by targeting EPAS1/SLC3A2 pathway

description: Additional file 2: Table S1. Upregulated genes in HA-VSMCs transfected with HCMV-miR-US33-5p mimics.
DOI: 10.6084/m9.figshare.19808496
title: Transcriptome analysis of eutopic endometrial stromal cells in women with adenomyosis by RNA-sequencing

description: This study aimed to identify differentially expressed genes (DEGs) and molecular pathways in eutopic endometrial stromal cells (EuESCs) from adenomyosis (AM) patients and to provide a new insight into the disease mechanisms. The gene expression profiles in adenomyotic EuESCs (A-EuESCs) and normal ESCs (N-ESCs) were analyzed by RNA-sequencing (RNA-Seq) and validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were performed to obtain insights into the functions of DEGs. The protein-protein interaction (PPI) network was constructed using the STRING database and visualized by Cytoscape software, and their hub genes were identified. A total of 458 up-/363 down-regulated genes were identified in A-EuESCs versus N-ESCs. The GO enrichment analysis showed that these genes were significantly enriched in calcium-dependent cell-cell adhesion. The most significant term of the KEGG pathway analysis was cytokine-cytokine receptor interaction. There were 145 nodes in the PPI network of the 157 DEGs, which were identified in significant enrichment pathway by the KEGG pathway analysis in N-ESCs and A-EuESCs. The PPI network revealed that IL-6 was a central hub gene. Besides, IL-6 was found as a central hub gene in the pro-inflammatory/chemotactic subnetwork, and EGF was noted as a central hub gene in the angiogenesis subnetwork. Our study indicated the alterations of transcriptomic profiles in A-EuESCs and provided new insights into the pathogenesis of AM. The A-EuESCs in women with AM have fundamental abnormalities that may predispose to pro-invasion/migration and angiogenesis.
DOI: 10.6084/m9.figshare.19808496.v1
title: Transcriptome analysis of eutopic endometrial stromal cells in women with adenomyosis by RNA-sequencing

description: This study aimed to identify differentially expressed genes (DEGs) and molecular pathways in eutopic endometrial stromal cells (EuESCs) from adenomyosis (AM) patients and to provide a new insight into the disease mechanisms. The gene expression profiles in adenomyotic EuESCs (A-EuESCs) and normal ESCs (N-ESCs) were analyzed by RNA-sequencing (RNA-Seq) and validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses were performed to obtain insights into the functions of DEGs. The protein-protein interaction (PPI) network was constructed using the STRING database and visualized by Cytoscape software, and their hub genes were identified. A total of 458 up-/363 down-regulated genes were identified in A-EuESCs versus N-ESCs. The GO enrichment analysis showed that these genes were significantly enriched in calcium-dependent cell-cell adhesion. The most significant term of the KEGG pathway analysis was cytokine-cytokine receptor interaction. There were 145 nodes in the PPI network of the 157 DEGs, which were identified in significant enrichment pathway by the KEGG pathway analysis in N-ESCs and A-EuESCs. The PPI network revealed that IL-6 was a central hub gene. Besides, IL-6 was found as a central hub gene in the pro-inflammatory/chemotactic subnetwork, and EGF was noted as a central hub gene in the angiogenesis subnetwork. Our study indicated the alterations of transcriptomic profiles in A-EuESCs and provided new insights into the pathogenesis of AM. The A-EuESCs in women with AM have fundamental abnormalities that may predispose to pro-invasion/migration and angiogenesis.
DOI: 10.6084/m9.figshare.19808119
title: Additional file 2 of HCMV-miR-US33-5p promotes apoptosis of aortic vascular smooth muscle cells by targeting EPAS1/SLC3A2 pathway

description: Additional file 2: Table S1. Upregulated genes in HA-VSMCs transfected with HCMV-miR-US33-5p mimics.
DOI: 10.6084/m9.figshare.19808122
title: Additional file 3 of HCMV-miR-US33-5p promotes apoptosis of aortic vascular smooth muscle cells by targeting EPAS1/SLC3A2 pathway

description: Additional file 3: Table S2. Downregulated genes in HA-VSMCs transfected with HCMV-miR-US33-5p mimics.