cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.13310197
title: Additional file 8 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 8: Table S4. Differentially abundant metabolites between AhRKO and WT mice fed LFD at week 8.
DOI: 10.6084/m9.figshare.13310197.v1
title: Additional file 8 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 8: Table S4. Differentially abundant metabolites between AhRKO and WT mice fed LFD at week 8.
DOI: 10.6084/m9.figshare.13310149.v1
title: Additional file 13 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 13: Table S9. Differentially abundant metabolites between AhRKO mice fed HFD and LFD at week 26.
DOI: 10.6084/m9.figshare.23271877
title: Statistical Significance of Clustering with Multidimensional Scaling

description: Clustering is a fundamental tool for exploratory data analysis. One central problem in clustering is deciding if the clusters discovered by clustering methods are reliable as opposed to being artifacts of natural sampling variation. Statistical significance of clustering (SigClust) is a recently developed cluster evaluation tool for high-dimension, low-sample size data. Despite its successful application to many scientific problems, there are cases where the original SigClust may not work well. Furthermore, for specific applications, researchers may not have access to the original data and only have the dissimilarity matrix. In this case, clustering is still a valuable exploratory tool, but the original SigClust is not applicable. To address these issues, we propose a new SigClust method using multidimensional scaling (MDS). The underlying idea behind MDS-based SigClust is that one can achieve low-dimensional representations of the original data via MDS using only the dissimilarity matrix and then apply SigClust on the low-dimensional MDS space. The proposed MDS-based SigClust can circumvent the challenge of parameter estimation of the original method in high-dimensional spaces while keeping the essential clustering structure in the MDS space. Both simulations and real data applications demonstrate that the proposed method works remarkably well for assessing the statistical significance of clustering. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.14883276.v1
title: LncRNA MIR22HG promotes osteoarthritis progression via regulating miR-9-3p/ADAMTS5 pathway

description: Dysregulation of long non-coding RNAs (lncRNAs) plays a fundamental role in the development and progression of osteoarthritis (OA), but the potential functions of lncRNAs in OA were not fully clarified. In the present work, we want to clarify the underlying functions and mechanisms of MIR22HG in OA. qRT-PCR was employed to detect the mRNA expression of MIR22HG, miR-9-3p, and ADAMTS5, while the protein expressions were measured using Western blot. The cell proliferation was examined through CCK8, while apoptosis was used in flow cytometry. Luciferase reporter assay and RNA immunoprecipitation (RIP) assays were undertaken to investigate the binding relationship among MIR22HG, ADAMTS5, and miR-9-3p. MIR22HG was significantly overexpressed in OA cartilages, OA chondrocytes and IL-1β-induced chondrocytes. Functionally, MIR22HG knockdown promoted cell proliferation, suppressed apoptosis, and contributed to downregulation of MMP13 and ADAMTS5 and upregulation of COL2A1 and ACAN in IL-1β-stimulated chondrocytes. Mechanistically, bioinformatic analysis indicated that MIR22HG may serve as a sponge for miR-9-3p and ADAMTS5 may be a potential targeted gene for miR-9-3p, which were subsequently verified through a dual-luciferase reporter assay. Moreover, rescue experiments showed that MIR22HG participated in the regulation of chondrocytes proliferation, apoptosis, and degradation of extracellular matrix via miR-9-3p/ADAMTS5 pathway. In conclusion, our findings illuminated that inhibition of MIR22HG ameliorated IL-1β-induced apoptosis and ECM degradation of human chondrocytes through miR-9-3p/ADAMTS5 pathway, which may provide a potentially promising target for OA treatment.
DOI: 10.6084/m9.figshare.13310155
title: Additional file 14 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 14: Table S10. Differentially abundant metabolites between WT mice fed HFD and LFD at week 26.
DOI: 10.25345/c5gq6rc9r
title: MassIVE MSV000094069 - Senescence of endothelial cells promotes phenotypic changes in adventitial fibroblasts: possible implications for vascular aging
title: Aging is the most important risk factor for the development of cardiovascular diseases. Senescent cells release plethora of factors commonly known as the senescence-associated secretory phenotype (SASP), which can modulate the normal function of the vascular wall. It is currently not well understood if and how endothelial cell senescence can affect adventitial niche. The aim of this study was to characterize oxidative stress-induced endothelial cells senescence and identify their paracrine effects on the primary cell type of the adventitia, the fibroblasts. Human aortic endothelial cells (HAEC) were treated with hydrogen peroxide to induce premature senescence. Mass spectrometry analysis identified several proteomic changes in senescent HAEC with top upregulated secretory protein growth differentiation factor 15 (GDF-15). Treatment of the human adventitial fibroblast cell line (hAdv cells) with conditioned medium (CM) from senescent HAEC resulted in alterations in the proteome of hAdv cells identified in mass spectrometry analysis. Majority of differentially expressed proteins in hAdv cells treated with CM from senescent HAEC were involved in the uptake and metabolism of lipoproteins, mitophagy and ferroptosis. We next analyzed if some of these changes and pathways might be regulated by GDF-15. We found that recombinant GDF-15 affected some ferroptosis-related factors (e.g. ferritin) and decreased oxidative stress in the analyzed adventitial fibroblast cell line, but it had no effect on erastin-induced cell death. Contrary, silencing of GDF-15 in hAdv cells was protective against this ferroptotic stimuli. Our findings provide a better understanding of the biology of senescent cells and can be of importance for potential therapeutic strategies targeting cell senescence or ferroptosis to alleviate vascular diseases.
DOI: 10.6084/m9.figshare.14883276
title: LncRNA MIR22HG promotes osteoarthritis progression via regulating miR-9-3p/ADAMTS5 pathway

description: Dysregulation of long non-coding RNAs (lncRNAs) plays a fundamental role in the development and progression of osteoarthritis (OA), but the potential functions of lncRNAs in OA were not fully clarified. In the present work, we want to clarify the underlying functions and mechanisms of MIR22HG in OA. qRT-PCR was employed to detect the mRNA expression of MIR22HG, miR-9-3p, and ADAMTS5, while the protein expressions were measured using Western blot. The cell proliferation was examined through CCK8, while apoptosis was used in flow cytometry. Luciferase reporter assay and RNA immunoprecipitation (RIP) assays were undertaken to investigate the binding relationship among MIR22HG, ADAMTS5, and miR-9-3p. MIR22HG was significantly overexpressed in OA cartilages, OA chondrocytes and IL-1β-induced chondrocytes. Functionally, MIR22HG knockdown promoted cell proliferation, suppressed apoptosis, and contributed to downregulation of MMP13 and ADAMTS5 and upregulation of COL2A1 and ACAN in IL-1β-stimulated chondrocytes. Mechanistically, bioinformatic analysis indicated that MIR22HG may serve as a sponge for miR-9-3p and ADAMTS5 may be a potential targeted gene for miR-9-3p, which were subsequently verified through a dual-luciferase reporter assay. Moreover, rescue experiments showed that MIR22HG participated in the regulation of chondrocytes proliferation, apoptosis, and degradation of extracellular matrix via miR-9-3p/ADAMTS5 pathway. In conclusion, our findings illuminated that inhibition of MIR22HG ameliorated IL-1β-induced apoptosis and ECM degradation of human chondrocytes through miR-9-3p/ADAMTS5 pathway, which may provide a potentially promising target for OA treatment.
DOI: 10.6084/m9.figshare.21506849
title: Additional file 3 of Three-dimensional microenvironment regulates gene expression, function, and tight junction dynamics of iPSC-derived blood–brain barrier microvessels

description: Additional file 3. Summary of tight junction dynamics data.
DOI: 10.6084/m9.figshare.23271877.v1
title: Statistical Significance of Clustering with Multidimensional Scaling

description: Clustering is a fundamental tool for exploratory data analysis. One central problem in clustering is deciding if the clusters discovered by clustering methods are reliable as opposed to being artifacts of natural sampling variation. Statistical significance of clustering (SigClust) is a recently developed cluster evaluation tool for high-dimension, low-sample size data. Despite its successful application to many scientific problems, there are cases where the original SigClust may not work well. Furthermore, for specific applications, researchers may not have access to the original data and only have the dissimilarity matrix. In this case, clustering is still a valuable exploratory tool, but the original SigClust is not applicable. To address these issues, we propose a new SigClust method using multidimensional scaling (MDS). The underlying idea behind MDS-based SigClust is that one can achieve low-dimensional representations of the original data via MDS using only the dissimilarity matrix and then apply SigClust on the low-dimensional MDS space. The proposed MDS-based SigClust can circumvent the challenge of parameter estimation of the original method in high-dimensional spaces while keeping the essential clustering structure in the MDS space. Both simulations and real data applications demonstrate that the proposed method works remarkably well for assessing the statistical significance of clustering. Supplemental materials for the article are available online.
DOI: 10.6084/m9.figshare.13310179
title: Additional file 3 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 3: Tables S1. Summary of the Wilcoxon rank sum test for the first three principal comments scores of PCA at both weeks 8 and 26.
DOI: 10.6084/m9.figshare.13310179.v1
title: Additional file 3 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 3: Tables S1. Summary of the Wilcoxon rank sum test for the first three principal comments scores of PCA at both weeks 8 and 26.
DOI: 10.6084/m9.figshare.13310191
title: Additional file 6 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 6: Table S2. Summary of the number of differentially abundant metabolites at both weeks 8 and 26.
DOI: 10.6084/m9.figshare.14883399
title: m6A RNA methylation regulators were associated with the malignancy and prognosis of ovarian cancer

description: N6-methyladenosine (m6A) RNA methylation regulators play a regulatory role in tumor pathogenesis and development. However, the role of m6A regulator genes in ovarian cancer (OC) has not been fully elucidated. This study aims to investigate the mRNA expressions, clinicopathological features, and prognostic values of m6A regulators in OC. Here, we demonstrate that the 17 m6A RNA methylation regulators are differentially expressed in ovarian cancer and normal tissues. By using consensus clustering, all ovarian cancer patients can be divided into two subgroups (cluster 1 and 2) based on the expression of 17 m6A RNA methylation regulators. Using Gene Set Enrichment Analysis, we identified that cluster 1 was most connected to oxidative phosphorylation pathways. Regression models identified that prognosis is associated with HNRNPA2B1, KIAA1429, and WTAP. qRT-PCR result show that the expression trends of HNRNPA2B1 and KIAA1429 are consistent with the predicted results. Multivariate Cox regression analysis results show that the risk score was an independent predictive factor in OV. The overall survival of high-risk patients was significantly shorter than that of low-risk patients. ROC curve analysis showed that the prognostic signature precisely predicted the 5-year survival of OV patients. A nomogram was developed to predict each patient’s survival probability and well calibrated and showed a satisfactory discrimination. Dendritic fraction, macrophage fraction, and neutrophil fraction showed higher fraction in high-risk patients. In conclusion, m6A RNA methylation regulators are vital participants in ovarian cancer pathology, and three-gene mRNA levels are valuable factors for prognosis predictions.
DOI: 10.6084/m9.figshare.13310191.v1
title: Additional file 6 of Effect of diet and intestinal AhR expression on fecal microbiome and metabolomic profiles

description: Additional file 6: Table S2. Summary of the number of differentially abundant metabolites at both weeks 8 and 26.
DOI: 10.6084/m9.figshare.19588872.v1
title: Additional file 14 of Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

description: Additional file 14: Supplementary Table 3. Number of sequence reads of the mapping analysis using the 707 virus genomes respectively against the 215 NGS data.
DOI: 10.6084/m9.figshare.19588872
title: Additional file 14 of Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses

description: Additional file 14: Supplementary Table 3. Number of sequence reads of the mapping analysis using the 707 virus genomes respectively against the 215 NGS data.
DOI: 10.21942/uva.25212896
title: Data for chapter 2 (part a)

description: Abstract: Many everyday activities are habitual. Among the most common human activities is communication. This paper experimentally studies two questions. First, we provide evidence that habits affect strategic communication in an unfamiliar environment. Second, we contrast two mechanisms through which habits operate, preference shaping and inattention. By varying the frequency of communicating in the unfamiliar environment, we find an effect only when the unfamiliar environment occurs rarely. Thus, our results favor the inattention mechanism. Our findings highlight the importance of accounting for habits, especially when studying human behavior in infrequent situations.The file contains the raw decision data from the experiment as exported by the software.
DOI: 10.21942/uva.25212896.v1
title: Data for chapter 2 (part a)

description: Abstract: Many everyday activities are habitual. Among the most common human activities is communication. This paper experimentally studies two questions. First, we provide evidence that habits affect strategic communication in an unfamiliar environment. Second, we contrast two mechanisms through which habits operate, preference shaping and inattention. By varying the frequency of communicating in the unfamiliar environment, we find an effect only when the unfamiliar environment occurs rarely. Thus, our results favor the inattention mechanism. Our findings highlight the importance of accounting for habits, especially when studying human behavior in infrequent situations.The file contains the raw decision data from the experiment as exported by the software.
DOI: 10.21942/uva.25212848
title: Data for chapter 2 (part b)

description: Abstract<b><i>:</i></b><b><i> </i></b>Many everyday activities are habitual. Among the most common human activities is communication. This paper experimentally studies two questions. First, we provide evidence that habits affect strategic communication in an unfamiliar environment. Second, we contrast two mechanisms through which habits operate, preference shaping and inattention. By varying the frequency of communicating in the unfamiliar environment, we find an effect only when the unfamiliar environment occurs rarely. Thus, our results favor the inattention mechanism. Our findings highlight the importance of accounting for habits, especially when studying human behavior in infrequent situations.The file contains decision times from the experiment
DOI: 10.21942/uva.25212848.v1
title: Data for chapter 2 (part b)

description: Abstract<b><i>:</i></b><b><i> </i></b>Many everyday activities are habitual. Among the most common human activities is communication. This paper experimentally studies two questions. First, we provide evidence that habits affect strategic communication in an unfamiliar environment. Second, we contrast two mechanisms through which habits operate, preference shaping and inattention. By varying the frequency of communicating in the unfamiliar environment, we find an effect only when the unfamiliar environment occurs rarely. Thus, our results favor the inattention mechanism. Our findings highlight the importance of accounting for habits, especially when studying human behavior in infrequent situations.The file contains decision times from the experiment
DOI: 10.21942/uva.25212791
title: Data for chapter 3

description: Abstract: We test whether anchoring affects people's elicited valuations for a bottle of wine in individual decision making and in markets. We anchor subjects by asking them if they are willing to sell a bottle of wine for a transparently uninformative random price. We elicit subjects' Willingness-To-Accept for the bottle before and after the market. Subjects participate in a double auction market either in a small or a large trading group. The variance in subjects' Willingness-To-Accept shrinks within trading groups. Our evidence supports the idea that markets have the potential to diminish anchoring effects. However, the market is not needed: our anchoring manipulation failed in a large sample. In a concise meta-analysis, we identify the circumstances under which anchoring effects of preferences can be expected.The file contains the raw experimental data as exported by the experimental software.<br><br>
DOI: 10.21942/uva.25212791.v1
title: Data for chapter 3

description: Abstract: We test whether anchoring affects people's elicited valuations for a bottle of wine in individual decision making and in markets. We anchor subjects by asking them if they are willing to sell a bottle of wine for a transparently uninformative random price. We elicit subjects' Willingness-To-Accept for the bottle before and after the market. Subjects participate in a double auction market either in a small or a large trading group. The variance in subjects' Willingness-To-Accept shrinks within trading groups. Our evidence supports the idea that markets have the potential to diminish anchoring effects. However, the market is not needed: our anchoring manipulation failed in a large sample. In a concise meta-analysis, we identify the circumstances under which anchoring effects of preferences can be expected.The file contains the raw experimental data as exported by the experimental software.<br><br>
DOI: 10.6084/m9.figshare.25211525
title: Datasets for visuliaztion in a genome browser for manuscript 'Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma'.

description: Datasets for visualization in UCSC Genome Browser of genome coverages of all generated next-generation sequencing data included in the manuscript ('Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma').
DOI: 10.6084/m9.figshare.25211525.v2
title: Datasets for visuliaztion in a genome browser for manuscript 'Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma'.

description: Datasets for visualization in UCSC Genome Browser of genome coverages of all generated next-generation sequencing data included in the manuscript ('Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma').
DOI: 10.6084/m9.figshare.13310590
title: Additional file 6 of Utility of a custom designed next generation DNA sequencing gene panel to molecularly classify endometrial cancers according to The Cancer Genome Atlas subgroups

description: Additional file 6. Table S6 - PrDSM pathogenicity scores for synonymous variants.
DOI: 10.5517/ccdc.csd.cc24w068
title: CCDC 1992159: Experimental Crystal Structure Determination

description: Related Article: haitao Yuan|2020|CSD Communication|||
description: Related Article: Xinkai Wang, Lili Song, Hefeng Guo|2022|J.Cluster Sci.|33|895|doi:10.1007/s10876-021-02027-2
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.cc2fsdn9
title: CCDC 2257781: Experimental Crystal Structure Determination

description: Related Article: Xing-Zi Li, Yu-Ping He, Hua Wu|2024|Angew.Chem.,Int.Ed.|63|e202317182|doi:10.1002/anie.202317182
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.cc2g88rs
title: CCDC 2272075: Experimental Crystal Structure Determination

description: Related Article: Samim Khan, Pubali Das, Sanobar Naaz, Paula Brandão, Aditya Choudhury, Raghavender Medishetty, Partha Pratim Ray, Mohammad Hedayetullah Mir|2023|Dalton Trans.|52|17934|doi:10.1039/D3DT02728G
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.cc2ghnc0
title: CCDC 2279162: Experimental Crystal Structure Determination

description: Related Article: Juan Yan, Guang-xiang Liu, Xiao-ming Ren|2009|Hecheng Huaxue|17|192|
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.cc2gl0fj
title: CCDC 2281427: Experimental Crystal Structure Determination

description: Related Article: Di-chang Zhong, Shao-ming Shi, Ji-hua Deng, Dong-qing Li, He-dong Bian, Zhen-feng Chen|2007|Guangxi Shifan Daxue Xuebao Ziran Kexueban|25|68|
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.