cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24136385
title: Additional file 1 of Impact of gallstone disease on the risk of stroke and coronary artery disease: evidence from prospective observational studies and genetic analyses

description: Additional file 1: Table S1. Characteristics of genetic instruments of gallstone disease. Table S2. Data sources, sample sizes, number of IVs. Table S3. The detailed search strategy for meta-analysis. Table S4. STROBE-MR checklist of recommended items to address in reports of Mendelian randomization studies. Table S5. Characteristics of included studies in meta-analysis. Table S6. Subgroup analyses for relationship between GSD and CVD. Table S7. Significant local regions after correcting for multiple testing (P &lt; 0.05/2,353). Table S8. Genome-wide significant SNPs identified by cross-trait meta-analysis between gallstone disease and stroke (P-CPASSOC &lt; 5×10-8, single trait P-value &lt; 1×10-3, clumping r2=0.2). Table S9. Genome-wide significant SNPs identified by cross-trait meta-analysis between gallstone disease and coronary artery disease (P-CPASSOC &lt; 5×10-8, single trait P-value &lt; 1×10-3, clumping r2=0.2). Table S10. Linear closest genes of each cross-trait analyses-identified SNP for gallstone disease and stroke. Table S11. Linear closest genes of each cross-trait analyses-identified SNP for gallstone disease and coronary artery disease. Table S12. List of SNPs in the 99% credible set identified from fine-mapping analysis for each CPASSOC-identified locus shared between gallstone disease and stroke. Table S13. List of SNPs in the 99% credible set identified from fine-mapping analysis for each CPASSOC-identified locus shared between gallstone disease and coronary artery disease. Table S14. Results from colocalization analysis for each pleiotropic locus identified from CPASSOC between gallstone disease and stroke. Table S15. Results from colocalization analysis for each pleiotropic locus identified from CPASSOC between gallstone disease and coronary artery disease. Table S16. Significant shared transcriptome-wide association analysis results between gallstone disease and coronary artery disease. Table S17. Baseline characteristics of UK Biobank participants by gallstone disease status during follow-up for stroke. Table S18. Baseline characteristics of UK Biobank participants by gallstone disease status during follow-up for coronary artery disease. Table S19. Observational associations between cholecystectomy and cardiovascular diseases. Table S20. Sex-specific observational associations between gallstone disease and cardiovascular diseases. Table S21. Observational associations between cardiovascular diseases and gallstone disease.
DOI: 10.6084/m9.figshare.20465310
title: <i>iProMix</i>: A Mixture Model for Studying the Function of ACE2 based on Bulk Proteogenomic Data

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over six million deaths in the ongoing COVID-19 pandemic. SARS-CoV-2 uses ACE2 protein to enter human cells, raising a pressing need to characterize proteins/pathways interacted with ACE2. Large-scale proteomic profiling technology is not mature at single-cell resolution to examine the protein activities in disease-relevant cell types. We propose <i>iProMix</i>, a novel statistical framework to identify epithelial-cell specific associations between ACE2 and other proteins/pathways with bulk proteomic data. <i>iProMix</i> decomposes the data and models cell type-specific conditional joint distribution of proteins through a mixture model. It improves cell-type composition estimation from prior input, and uses a nonparametric inference framework to account for uncertainty of cell-type proportion estimates in hypothesis test. Simulations demonstrate <i>iProMix</i> has well-controlled false discovery rates and favorable powers in nonasymptotic settings. We apply <i>iProMix</i> to the proteomic data of 110 (tumor-adjacent) normal lung tissue samples from the Clinical Proteomic Tumor Analysis Consortium lung adenocarcinoma study, and identify interferon α/γ response pathways as the most significant pathways associated with ACE2 protein abundances in epithelial cells. Strikingly, the association direction is sex-specific. This result casts light on the sex difference of COVID-19 incidences and outcomes, and motivates sex-specific evaluation for interferon therapies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.24136385.v1
title: Additional file 1 of Impact of gallstone disease on the risk of stroke and coronary artery disease: evidence from prospective observational studies and genetic analyses

description: Additional file 1: Table S1. Characteristics of genetic instruments of gallstone disease. Table S2. Data sources, sample sizes, number of IVs. Table S3. The detailed search strategy for meta-analysis. Table S4. STROBE-MR checklist of recommended items to address in reports of Mendelian randomization studies. Table S5. Characteristics of included studies in meta-analysis. Table S6. Subgroup analyses for relationship between GSD and CVD. Table S7. Significant local regions after correcting for multiple testing (P &lt; 0.05/2,353). Table S8. Genome-wide significant SNPs identified by cross-trait meta-analysis between gallstone disease and stroke (P-CPASSOC &lt; 5×10-8, single trait P-value &lt; 1×10-3, clumping r2=0.2). Table S9. Genome-wide significant SNPs identified by cross-trait meta-analysis between gallstone disease and coronary artery disease (P-CPASSOC &lt; 5×10-8, single trait P-value &lt; 1×10-3, clumping r2=0.2). Table S10. Linear closest genes of each cross-trait analyses-identified SNP for gallstone disease and stroke. Table S11. Linear closest genes of each cross-trait analyses-identified SNP for gallstone disease and coronary artery disease. Table S12. List of SNPs in the 99% credible set identified from fine-mapping analysis for each CPASSOC-identified locus shared between gallstone disease and stroke. Table S13. List of SNPs in the 99% credible set identified from fine-mapping analysis for each CPASSOC-identified locus shared between gallstone disease and coronary artery disease. Table S14. Results from colocalization analysis for each pleiotropic locus identified from CPASSOC between gallstone disease and stroke. Table S15. Results from colocalization analysis for each pleiotropic locus identified from CPASSOC between gallstone disease and coronary artery disease. Table S16. Significant shared transcriptome-wide association analysis results between gallstone disease and coronary artery disease. Table S17. Baseline characteristics of UK Biobank participants by gallstone disease status during follow-up for stroke. Table S18. Baseline characteristics of UK Biobank participants by gallstone disease status during follow-up for coronary artery disease. Table S19. Observational associations between cholecystectomy and cardiovascular diseases. Table S20. Sex-specific observational associations between gallstone disease and cardiovascular diseases. Table S21. Observational associations between cardiovascular diseases and gallstone disease.
DOI: 10.6084/m9.figshare.20465310.v3
title: <i>iProMix</i>: A Mixture Model for Studying the Function of ACE2 based on Bulk Proteogenomic Data

description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over six million deaths in the ongoing COVID-19 pandemic. SARS-CoV-2 uses ACE2 protein to enter human cells, raising a pressing need to characterize proteins/pathways interacted with ACE2. Large-scale proteomic profiling technology is not mature at single-cell resolution to examine the protein activities in disease-relevant cell types. We propose <i>iProMix</i>, a novel statistical framework to identify epithelial-cell specific associations between ACE2 and other proteins/pathways with bulk proteomic data. <i>iProMix</i> decomposes the data and models cell type-specific conditional joint distribution of proteins through a mixture model. It improves cell-type composition estimation from prior input, and uses a nonparametric inference framework to account for uncertainty of cell-type proportion estimates in hypothesis test. Simulations demonstrate <i>iProMix</i> has well-controlled false discovery rates and favorable powers in nonasymptotic settings. We apply <i>iProMix</i> to the proteomic data of 110 (tumor-adjacent) normal lung tissue samples from the Clinical Proteomic Tumor Analysis Consortium lung adenocarcinoma study, and identify interferon α/γ response pathways as the most significant pathways associated with ACE2 protein abundances in epithelial cells. Strikingly, the association direction is sex-specific. This result casts light on the sex difference of COVID-19 incidences and outcomes, and motivates sex-specific evaluation for interferon therapies. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.7358132
title: Aflatoxin B<sub>1</sub> in peanut oil from Western Guangdong, China, during 2016–2017

description: Aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) occurrence in peanut oil samples randomly collected from family workshops in western Guangdong during 2016–2017 (<i>n</i> = 427) was surveyed. AFB<sub>1</sub> content was screened by enzyme-linked immunosorbent assay (ELISA) protocol and analytically confirmed with an UPLC-MS/MS method. The limit of detection of the ELISA method was 1.08 μg kg<sup>−1</sup>. The recovery values ranged from 84.4 to 92.6% with relative standard deviations of 2.2 to 4.8%. AFB<sub>1</sub> was quantified in 47 samples (22.5%) with a range of 15.4–49.9 μg kg<sup>−1</sup> in 2016 and in 33 samples (15.1%) with 8.8–22.2 μg kg<sup>−1</sup> in 2017, respectively. The AFB<sub>1</sub> contamination in peanut oil was season-depended in western Guangdong with the worst case in spring (24.2–37.9%). Overall, a significant reduction of AFB<sub>1</sub> occurrence was observed in western Guangdong after 2016. It is advisable to control AFB<sub>1</sub> in bulk and self-pressed oil from family workshops and regulate it mandatorily if necessary.
DOI: 10.6084/m9.figshare.13125277.v1
title: Pygmaeomycetaceae, a new root-associated family in Mucoromycotina from the pygmy pine plains

description: A new genus, <i>Pygmaeomyces</i>, and two new species are described based on phylogenetic analyses and phenotypic and ecological characters. The species delimitation was based on concordance of gene genealogies. The <i>Pygmaeomyces</i> cultures were isolated from the roots of mountain laurel (<i>Kalmia latifolia</i>) and pitch pine (<i>Pinus rigida</i>) from the acidic and oligotrophic New Jersey pygmy pine plains; however, they likely have a broader distribution because their internal transcribed spacer (ITS) sequences have high similarity to a number of environmental sequences from multiple independent studies. Based on the phylogeny and phenotypic characters, a new family, Pygmaeomycetaceae, is proposed to accommodate this new lineage in Mucoromycotina. Pygmaeomycetaceae corresponds to Clade GS23, which was identified based on a sequence-only soil fungal survey and was believed to be a distinct new class. Compared with the culture-based methods, we observed that sequence-only analyses tend to overestimate the taxonomic level. Results from this work will facilitate ecological and evolutionary studies on root-associated fungi.
DOI: 10.6084/m9.figshare.7358132.v1
title: Aflatoxin B<sub>1</sub> in peanut oil from Western Guangdong, China, during 2016–2017

description: Aflatoxin B<sub>1</sub> (AFB<sub>1</sub>) occurrence in peanut oil samples randomly collected from family workshops in western Guangdong during 2016–2017 (<i>n</i> = 427) was surveyed. AFB<sub>1</sub> content was screened by enzyme-linked immunosorbent assay (ELISA) protocol and analytically confirmed with an UPLC-MS/MS method. The limit of detection of the ELISA method was 1.08 μg kg<sup>−1</sup>. The recovery values ranged from 84.4 to 92.6% with relative standard deviations of 2.2 to 4.8%. AFB<sub>1</sub> was quantified in 47 samples (22.5%) with a range of 15.4–49.9 μg kg<sup>−1</sup> in 2016 and in 33 samples (15.1%) with 8.8–22.2 μg kg<sup>−1</sup> in 2017, respectively. The AFB<sub>1</sub> contamination in peanut oil was season-depended in western Guangdong with the worst case in spring (24.2–37.9%). Overall, a significant reduction of AFB<sub>1</sub> occurrence was observed in western Guangdong after 2016. It is advisable to control AFB<sub>1</sub> in bulk and self-pressed oil from family workshops and regulate it mandatorily if necessary.
DOI: 10.6084/m9.figshare.7357895.v2
title: Luteolin inhibits Musashi1 binding to RNA and disrupts cancer phenotypes in glioblastoma cells

description: RNA binding proteins have emerged as critical oncogenic factors and potential targets in cancer therapy. In this study, we evaluated Musashi1 (Msi1) targeting as a strategy to treat glioblastoma (GBM); the most aggressive brain tumor type. Msi1 expression levels are often high in GBMs and other tumor types and correlate with poor clinical outcome. Moreover, Msi1 has been implicated in chemo- and radio-resistance. Msi1 modulates a range of cancer relevant processes and pathways and regulates the expression of stem cell markers and oncogenic factors via mRNA translation/stability. To identify Msi1 inhibitors capable of blocking its RNA binding function, we performed a ~25,000 compound fluorescence polarization screen. NMR and LSPR were used to confirm direct interaction between Msi1 and luteolin, the leading compound. Luteolin displayed strong interaction with Msi1 RNA binding domain 1 (RBD1). As a likely consequence of this interaction, we observed via western and luciferase assays that luteolin treatment diminished Msi1 positive impact on the expression of pro-oncogenic target genes. We tested the effect of luteolin treatment on GBM cells and showed that it reduced proliferation, cell viability, colony formation, migration and invasion of U251 and U343 GBM cells. Luteolin also decreased the proliferation of patient-derived glioma initiating cells (GICs) and tumor-organoids but did not affect normal astrocytes. Finally, we demonstrated the value of combined treatments with luteolin and olaparib (PARP inhibitor) or ionizing radiation (IR). Our results show that luteolin functions as an inhibitor of Msi1 and demonstrates its potential use in GBM therapy.
DOI: 10.6084/m9.figshare.7357895.v1
title: Luteolin inhibits Musashi1 binding to RNA and disrupts cancer phenotypes in glioblastoma cells

description: RNA binding proteins have emerged as critical oncogenic factors and potential targets in cancer therapy. In this study, we evaluated Musashi1 (Msi1) targeting as a strategy to treat glioblastoma (GBM); the most aggressive brain tumor type. Msi1 expression levels are often high in GBMs and other tumor types and correlate with poor clinical outcome. Moreover, Msi1 has been implicated in chemo- and radio-resistance. Msi1 modulates a range of cancer relevant processes and pathways and regulates the expression of stem cell markers and oncogenic factors via mRNA translation/stability. To identify Msi1 inhibitors capable of blocking its RNA binding function, we performed a ~ 25,000 compound fluorescence polarization screen. NMR and LSPR were used to confirm direct interaction between Msi1 and luteolin, the leading compound. Luteolin displayed strong interaction with Msi1 RNA binding domain 1 (RBD1). As a likely consequence of this interaction, we observed via western and luciferase assays that luteolin treatment diminished Msi1 positive impact on the expression of pro-oncogenic target genes. We tested the effect of luteolin treatment on GBM cells and showed that it reduced proliferation, cell viability, colony formation, migration and invasion of U251 and U343 GBM cells. Luteolin also decreased the proliferation of patient-derived glioma initiating cells (GICs) and tumor-organoids but did not affect normal astrocytes. Finally, we demonstrated the value of combined treatments with luteolin and olaparib (PARP inhibitor) or ionizing radiation (IR). Our results show that luteolin functions as an inhibitor of Msi1 and demonstrates its potential use in GBM therapy.
DOI: 10.6084/m9.figshare.13126358
title: Research Dataset.xlsx

description: This dataset includes major and trace elements, Sr-Nd-Fe isotopes for Neoproterozoic basaltic to andesitic dikes from the Yangtze Block, South China.
DOI: 10.6084/m9.figshare.13647044
title: Additional file 4 of Hypoxia promotes the metastasis of pancreatic cancer through regulating NOX4/KDM5A-mediated histone methylation modification changes in a HIF1A-independent manner

description: Additional file 4. Supplementary Table 1. Hypoxia score of the pancreatic cancer samples in TCGA.
DOI: 10.6084/m9.figshare.13647050.v1
title: Additional file 6 of Hypoxia promotes the metastasis of pancreatic cancer through regulating NOX4/KDM5A-mediated histone methylation modification changes in a HIF1A-independent manner

description: Additional file 6. Supplementary Table 3. Genes positively related to hypoxia score using pearson correlation analyse in TCGA PAAD samples.
DOI: 10.6084/m9.figshare.11553513
title: Raw data.zip

description: Dynamic changes of
intestinal microbiota of young forest musk deer during weaning

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DOI: 10.6084/m9.figshare.6832895.v1
title: Frozen-to-jamming-to-fluid Transition of Weakly Sheared Granular Systems by Low-frequency Mechanical Spectroscopy

description: Granular matter usually displays frozen, jamming and fluidized states when submitted to an external vibration with increasing intensity. The dissipation properties of granular systems with three different millimeter-size glass grains (0.1, 0.5 and 1.9 mm) have been investigated by a modified low-frequency inverted torsion pendulum under a shear strain and an external pressure. With increasing the immersed depth of the oscillating probe, all the systems show the frozen, jamming and fluidized behaviors. Furthermore, the critical depth at which the transition occurs increases with increasing grain size, but decreases with the application of pressure. A qualitative explanation is tentatively proposed to understand the underlying mechanism of complex viscoelastic properties of the glass particle systems.
DOI: 10.6084/m9.figshare.12601255.v1
title: Propensity Score Matched Analysis Comparing Robotic-Assisted with Laparoscopic Posterior Retroperitoneal Adrenalectomy

description: To compare the perioperative outcomes between robotic posterior retroperitoneal adrenalectomy (RPRA) with laparoscopic posterior retroperitoneal adrenalectomy (LPRA) for adrenal tumors and to identify which group of patients may benefit from RPRA. A total of 401 patients who fulfilled the inclusion criteria were collected and analyzed; among them, 86 and 315 patients underwent RPRA and LPRA, respectively. To adjust for potential baseline confounders, propensity score matching (PSM) was conducted at a 1:1 ratio. Patient demographics and perioperative outcomes were compared between the two groups. After matching, no differences were found between the two groups in patient demographics or tumor characteristics. The median length of postoperative stay (3 vs. 4 days, <i>p</i> = 0.001) was significantly shorter in the RPRA group, but this group also showed a higher median total hospitalization cost (8121.89 vs. 4107.92 $, <i>p</i> &lt; 0.001). There was no difference in the median operative duration (100 vs. 110 min, <i>p</i> = 0.554), median estimated blood loss (50 vs. 50 ml, <i>p</i> = 0.730), transfusion rate (<i>p</i> = 0.497) or incidence of postoperative complications (<i>p</i> = 0.428). According to our research, RPRA leads to a shorter postoperative hospitalization stay but a higher total hospitalization cost than LPRA after propensity score matching.
DOI: 10.6084/m9.figshare.12601270
title: Analysis of treatment cost for neuroblastoma to the family: a single-center cross-sectional study in China

description: Neuroblastoma (NB) is notorious in childhood cancer because of its high incidence and poor prognosis. The Children’s Oncology Group reported that the 3-year OS in the high-risk (HR) group is 50%, and the HR-NB with bone marrow metastasis in our center is 43.1%. Thousands of families in China suffer from the cost of NB, but the true costs of therapy are unknown; to date, no study has ever performed a detailed therapy costs analysis for NB. The objective of this study was to assess the economic burden of NB treatment in children to the family, to ultimately reduce related expenses for patients and promote the establishment of NB management policy. Data in this cross-sectional study were collected via questionnaires completed by parents at the outpatient clinic and was verified via a computer system. Therapy costs of children with NB of differing risks were analyzed through descriptive statistics (1 CNY ≈ 0.1412 USD). Median direct medical costs of low risk (LR), middle risk (MR), and HR NB during treatment were 180.0 (120.0, 300.0), 200.0 (166.0, 300.0), and 650.0 (415.5, 850.0) thousand Chinese yuan (CNY), respectively. Direct non-medical costs including transportation, food, and accommodation were 60.0 (37.0, 100.0), 80.0 (60.0, 120.0), and 100.0 (80.0, 157.5) thousand CNY in the LR, MR, and HR groups, respectively. Additionally, parents accrued work absences to attend treatment, and lost a total of 100.0 (50.0, 150.0) thousand CNY in indirect costs. Families whose children had relapsed or died were excluded from this analysis and therefore limited the conclusions drawn. Parents were asked to recall costs since initial diagnosis (1–6 years in the past), but this extended time period may have introduced recall bias. Direct non-medical and indirect costs play an important role in the total treatment costs of NB. Children with NB treated in local hospitals and followed up in hospital specialized in childhood oncology may save many unnecessary expenses. China's healthcare system should establish mechanisms and provide financial support for children with NB.
DOI: 10.6084/m9.figshare.25150919
title: The statistics for the factor analysis of the IFRS transition

description: The research is based on the recent IMD statistics (2023). In general, the data studied belong to the period 2020–2023. The sample includes 52 countries for which the values of all indicators are given in the IMD (2023) materials, which is necessary for forming a data array without gaps, which is a prerequisite for regression analysis.
DOI: 10.6084/m9.figshare.25150919.v4
title: The statistics for the factor analysis of the IFRS transition

description: The research is based on the recent IMD statistics (2023). In general, the data studied belong to the period 2020–2023. The sample includes 52 countries for which the values of all indicators are given in the IMD (2023) materials, which is necessary for forming a data array without gaps, which is a prerequisite for regression analysis.
DOI: 10.6084/m9.figshare.25150919.v3
title: The statistics for the factor analysis of the IFRS transition

description: The research is based on the recent IMD statistics (2023). In general, the data studied belong to the period 2020–2023. The sample includes 52 countries for which the values of all indicators are given in the IMD (2023) materials, which is necessary for forming a data array without gaps, which is a prerequisite for regression analysis.