cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.20131046.v1
title: Additional file 8 of Construction and validation of molecular subtypes of coronary artery disease based on ferroptosis-related genes

description: Additional file 8: Table S5. Statistical analysis of immune cell infiltration in different subgroups based on single-sample gene set enrichment analysis (ssGSEA).
DOI: 10.6084/m9.figshare.20131018.v1
title: Additional file 3 of Potential biomarkers of spinal dural arteriovenous fistula: C4BPA and C1QA

description: Additional file 3: Table S2. The comparison of baseline characteristics.
DOI: 10.6084/m9.figshare.20131021
title: Additional file 4 of Potential biomarkers of spinal dural arteriovenous fistula: C4BPA and C1QA

description: Additional file 4: Table S3. The result of protein quantification and differential analysis.
DOI: 10.6084/m9.figshare.20652139
title: Additional file 4 of Exploring Lead loci shared between schizophrenia and Cardiometabolic traits

description: Additional file 4. Additional Tables.
DOI: 10.6084/m9.figshare.12263762
title: Additional file 5 of The effect of antibiotics on the gut microbiome: a metagenomics analysis of microbial shift and gut antibiotic resistance in antibiotic treated mice

description: Additional file 5: Supplementary Table 5. Ciprofloxacin species relative abundance.
DOI: 10.6084/m9.figshare.20652139.v1
title: Additional file 4 of Exploring Lead loci shared between schizophrenia and Cardiometabolic traits

description: Additional file 4. Additional Tables.
DOI: 10.6084/m9.figshare.10693562.v1
title: Quality control and other metadata of Danish dataset.

description: Metadata and quality control information associated with the Danish Salmonella Typhimurium dataset collected to develop WGS-based source attribution methods.
DOI: 10.6084/m9.figshare.10693568
title: Quality control and other metadata of German dataset.

description: Metadata and quality control information associated with the German Salmonella Typhimurium dataset collected to develop WGS-based source attribution methods.
DOI: 10.5281/zenodo.10648191
title: Dataset related to the article "Prevalence and prognosis of structural heart disease among athletes with negative T waves and normal transthoracic echocardiography"

description: This record contains raw data related to the article "Prevalence and prognosis of structural heart disease among athletes with negative T waves and normal transthoracic echocardiography"

Introduction The aim of the present study was to evaluate the prevalence and prognosis of structural heart disease (SHD) among competitive athletes with negative T waves without pathological findings at transthoracic echocardiogram. Methods From a prospective register of 450 athletes consecutively evaluated during a second-level cardiological examination, we retrospectively identified all subjects with the following inclusion criteria: (1) not previously known cardiovascular disease; (2) negative T waves in leads other than V1–V2; (3) normal transthoracic echocardiogram. Patients underwent cardiac MRI and CT. The primary endpoint was the diagnosis of definite SHD after multimodality imaging evaluation. A follow-up was collected for a combined end-point of sudden death, resuscitated sudden cardiac death and hospitalization for any cardiovascular causes. Results A total of 55 competitive athletes were finally enrolled (50 males, 90%) with a mean age of 27.5 ± 14.1 years. Among the population enrolled 16 (29.1%) athletes had a final diagnosis of SHD. At multivariate analysis, only deep negative T waves remained statistically significant [OR (95% CI) 7.81 (1.24–49.08), p = 0.0285]. Contemporary identification of deep negative T waves and complex arrhythmias in the same patients appeared to have an incremental diagnostic value. No events were collected at 49.3 ± 12.3 months of follow-up. Conclusions In a cohort of athletes with negative T waves at ECG, cardiac MRI (and selected use of cardiac CT) enabled the identification of 16 (29.1%) subjects with SHD despite normal transthoracic echocardiography. Deep negative T waves and complex ventricular arrhythmias were the only clinical characteristic associated with SHD diagnosis.
DOI: 10.5281/zenodo.10648192
title: Dataset related to the article "Prevalence and prognosis of structural heart disease among athletes with negative T waves and normal transthoracic echocardiography"

description: This record contains raw data related to the article "Prevalence and prognosis of structural heart disease among athletes with negative T waves and normal transthoracic echocardiography"

Introduction The aim of the present study was to evaluate the prevalence and prognosis of structural heart disease (SHD) among competitive athletes with negative T waves without pathological findings at transthoracic echocardiogram. Methods From a prospective register of 450 athletes consecutively evaluated during a second-level cardiological examination, we retrospectively identified all subjects with the following inclusion criteria: (1) not previously known cardiovascular disease; (2) negative T waves in leads other than V1–V2; (3) normal transthoracic echocardiogram. Patients underwent cardiac MRI and CT. The primary endpoint was the diagnosis of definite SHD after multimodality imaging evaluation. A follow-up was collected for a combined end-point of sudden death, resuscitated sudden cardiac death and hospitalization for any cardiovascular causes. Results A total of 55 competitive athletes were finally enrolled (50 males, 90%) with a mean age of 27.5 ± 14.1 years. Among the population enrolled 16 (29.1%) athletes had a final diagnosis of SHD. At multivariate analysis, only deep negative T waves remained statistically significant [OR (95% CI) 7.81 (1.24–49.08), p = 0.0285]. Contemporary identification of deep negative T waves and complex arrhythmias in the same patients appeared to have an incremental diagnostic value. No events were collected at 49.3 ± 12.3 months of follow-up. Conclusions In a cohort of athletes with negative T waves at ECG, cardiac MRI (and selected use of cardiac CT) enabled the identification of 16 (29.1%) subjects with SHD despite normal transthoracic echocardiography. Deep negative T waves and complex ventricular arrhythmias were the only clinical characteristic associated with SHD diagnosis.
DOI: 10.6084/m9.figshare.20131024
title: Additional file 5 of Potential biomarkers of spinal dural arteriovenous fistula: C4BPA and C1QA

description: Additional file 5: Table S4. The result of GO/KEGG enrichment in CSF sample.
DOI: 10.5281/zenodo.10648242
title: Partial dataset related to the article "Stress-only dynamic computed tomography perfusion protocol (CTP) alone without computed tomography coronary angiography (CCTA) has limited specificity to diagnose ischemia: A retrospective two-center study."

description: This record contains partial raw data related to the article “Stress-only dynamic computed tomography perfusion protocol (CTP) alone without computed tomography coronary angiography (CCTA) has limited specificity to diagnose ischemia: A retrospective two-center study” 

Purpose: To investigate diagnostic performance of stress-only dynamic myocardial computed tomography perfusion (CTP) without computed tomography coronary angiography (CCTA) to diagnose ischemia with invasive fractional flow reserve (FFR) as a reference standard. Method: 135 datasets (68 positive for ischemia with invasive FFR < 0.8) acquired with a 256-slice CT system (Revolution, GE Healthcare, Chicago, IL, USA) were retrieved, postprocessed with a deep learning-based algorithm (Advanced intelligent Clear-IQ Engine (AiCE), Canon Medical Systems, Otawara, Japan) (FC03/cardiac kernel, 8 mm slice thickness), analyzed using a dedicated workstation (Vitrea research 7.11.0. Vital Images, Minnetonka, MN, USA), and loaded into a clinical workstation (CardIQ, GE Healthcare, Chicago, IL, USA) for review. Ten observers with various experience from two research sites evaluated the post-processed images, perfusion slices and maps to indicate presence vs absence of perfusion defect and its probability (five-point Likert scale). Binary decisions and probability scores were used to calculate sensitivity and specificity for each reader, and to create receiver operating characteristics (ROC) curves, respectively. Furthermore, the correlation coefficient (ICC) was computed. ROC AUC of a purely quantitative analysis was obtained thanks to a color-coded map with a fixed scale superimposed on myocardial walls displaying myocardial blood flow (MBF) values. Results: The overall case-based sensitivity and specificity for the detection of perfusion deficit were 0.79 and 0.30, respectively. No significant differences were detected in the AUC across readers (p value = 0.66). The AUC values were 0.50, 0.58, 0.63, 0.59, 0.45, 0.60, 0.56, 0.61, 0.52, 0.61. Absolute reader agreement ICC was 0.60 (good agreement) for an average case. Conclusion: Dynamic CTP alone has good sensitivity, but low specificity when analyzed without CCTA. These findings reinforce the need to guide the interpretation functional test with the knowledge of coronary artery anatomy.
DOI: 10.5281/zenodo.10648243
title: Partial dataset related to the article "Stress-only dynamic computed tomography perfusion protocol (CTP) alone without computed tomography coronary angiography (CCTA) has limited specificity to diagnose ischemia: A retrospective two-center study."

description: This record contains partial raw data related to the article “Stress-only dynamic computed tomography perfusion protocol (CTP) alone without computed tomography coronary angiography (CCTA) has limited specificity to diagnose ischemia: A retrospective two-center study” 

Purpose: To investigate diagnostic performance of stress-only dynamic myocardial computed tomography perfusion (CTP) without computed tomography coronary angiography (CCTA) to diagnose ischemia with invasive fractional flow reserve (FFR) as a reference standard. Method: 135 datasets (68 positive for ischemia with invasive FFR < 0.8) acquired with a 256-slice CT system (Revolution, GE Healthcare, Chicago, IL, USA) were retrieved, postprocessed with a deep learning-based algorithm (Advanced intelligent Clear-IQ Engine (AiCE), Canon Medical Systems, Otawara, Japan) (FC03/cardiac kernel, 8 mm slice thickness), analyzed using a dedicated workstation (Vitrea research 7.11.0. Vital Images, Minnetonka, MN, USA), and loaded into a clinical workstation (CardIQ, GE Healthcare, Chicago, IL, USA) for review. Ten observers with various experience from two research sites evaluated the post-processed images, perfusion slices and maps to indicate presence vs absence of perfusion defect and its probability (five-point Likert scale). Binary decisions and probability scores were used to calculate sensitivity and specificity for each reader, and to create receiver operating characteristics (ROC) curves, respectively. Furthermore, the correlation coefficient (ICC) was computed. ROC AUC of a purely quantitative analysis was obtained thanks to a color-coded map with a fixed scale superimposed on myocardial walls displaying myocardial blood flow (MBF) values. Results: The overall case-based sensitivity and specificity for the detection of perfusion deficit were 0.79 and 0.30, respectively. No significant differences were detected in the AUC across readers (p value = 0.66). The AUC values were 0.50, 0.58, 0.63, 0.59, 0.45, 0.60, 0.56, 0.61, 0.52, 0.61. Absolute reader agreement ICC was 0.60 (good agreement) for an average case. Conclusion: Dynamic CTP alone has good sensitivity, but low specificity when analyzed without CCTA. These findings reinforce the need to guide the interpretation functional test with the knowledge of coronary artery anatomy.
DOI: 10.6084/m9.figshare.20131043
title: Additional file 7 of Construction and validation of molecular subtypes of coronary artery disease based on ferroptosis-related genes

description: Additional file 7: Table S4. All signal pathways obtained by gene set enrichment analysis (GSEA).
DOI: 10.6084/m9.figshare.20131049
title: Additional file 9 of Construction and validation of molecular subtypes of coronary artery disease based on ferroptosis-related genes

description: Additional file 9: Table S6. Ferroptosis-related genes identified by least absolute shrinkage and selection operator (LASSO) regression.
DOI: 10.6084/m9.figshare.20131423.v1
title: Pancreatic cancer cell exosomes induce lipidomics changes in adipocytes

description: Increasing evidence has demonstrated the important roles of exosomes during pancreatic cancer development. However, the effects of pancreatic cancer exosomes (PC-exos) on adipocytes remain largely unknown. Here, we used mass-spectrometry-based lipidomics to identify lipids that were changed in adipocytes after exposure to PC-exos, and we found that triglyceride (TG) reduction was the most significant, which might be induced by increased lipolysis because the number of large lipid droplets increased while small ones decreased. Additionally, abdominal adipocytes in mice injected with PC-exos had a relatively smaller size. Mechanistically, we found that genes involved in metabolism and inflammation were up-regulated, among which increase of IL-6 was significant, and we then found IL-6 promoted lipolysis. To our knowledge, this is the first study on the lipidomics changes of adipocytes after PC-exos treatment.
DOI: 10.6084/m9.figshare.14363463
title: ATG14 and RB1CC1 play essential roles in maintaining muscle homeostasis

description: Defects in macroautophagy/autophagy are implicated in the pathogenesis of neuromuscular and heart diseases. To precisely define the roles of autophagy-related genes in skeletal and cardiac muscles, we generated muscle-specific <i>rb1cc1-</i> and <i>atg14-</i>conditional knockout (cKO) mice by using <i>Ckm/Ckmm2-Cre</i> and compared their phenotypes to those of <i>ulk1 ulk2</i>-conditional double-knockout (cDKO) mice. <i>atg14</i>-cKO mice developed hypertrophic cardiomyopathy, which was associated with abnormal accumulation of autophagic cargoes in the heart and early mortality. Skeletal muscles of both <i>atg14</i>-cKO and <i>rb1cc1</i>-cKO mice showed features of autophagic vacuolar myopathy with ubiquitin<sup>+</sup> SQSTM1<sup>+</sup> deposits, but only those of <i>rb1cc1</i>-cKO mice showed TARDBP/TDP-43<sup>+</sup> pathology and other features of the inclusion body myopathy–like disease we previously described in <i>ulk1 ulk2</i>-cDKO mice. Herein, we highlight tissue-specific differences between skeletal and cardiac muscles in their reliance on core autophagy proteins and unique roles for ULK1-ULK2 and RB1CC1 among these proteins in the development of TARDBP<sup>+</sup> pathology. <b>ABBREVIATIONS</b>:AVM: autophagic vacuolar myopathy; cDKO: conditional double knockout; cKO: conditional knockout; H&E: hematoxylin and eosin; IBM: inclusion body myopathy; mtDNA: mitochondrial DNA; PFA: paraformaldehyde; RNP: ribonucleoprotein; TBST: Tris-buffered saline with 0.2% Triton X-100
DOI: 10.6084/m9.figshare.14363463.v1
title: ATG14 and RB1CC1 play essential roles in maintaining muscle homeostasis

description: Defects in macroautophagy/autophagy are implicated in the pathogenesis of neuromuscular and heart diseases. To precisely define the roles of autophagy-related genes in skeletal and cardiac muscles, we generated muscle-specific <i>rb1cc1-</i> and <i>atg14-</i>conditional knockout (cKO) mice by using <i>Ckm/Ckmm2-Cre</i> and compared their phenotypes to those of <i>ulk1 ulk2</i>-conditional double-knockout (cDKO) mice. <i>atg14</i>-cKO mice developed hypertrophic cardiomyopathy, which was associated with abnormal accumulation of autophagic cargoes in the heart and early mortality. Skeletal muscles of both <i>atg14</i>-cKO and <i>rb1cc1</i>-cKO mice showed features of autophagic vacuolar myopathy with ubiquitin<sup>+</sup> SQSTM1<sup>+</sup> deposits, but only those of <i>rb1cc1</i>-cKO mice showed TARDBP/TDP-43<sup>+</sup> pathology and other features of the inclusion body myopathy–like disease we previously described in <i>ulk1 ulk2</i>-cDKO mice. Herein, we highlight tissue-specific differences between skeletal and cardiac muscles in their reliance on core autophagy proteins and unique roles for ULK1-ULK2 and RB1CC1 among these proteins in the development of TARDBP<sup>+</sup> pathology. <b>ABBREVIATIONS</b>:AVM: autophagic vacuolar myopathy; cDKO: conditional double knockout; cKO: conditional knockout; H&E: hematoxylin and eosin; IBM: inclusion body myopathy; mtDNA: mitochondrial DNA; PFA: paraformaldehyde; RNP: ribonucleoprotein; TBST: Tris-buffered saline with 0.2% Triton X-100
DOI: 10.6084/m9.figshare.14363466.v1
title: 4DNvestigator: Time Series Genomic Data Analysis Toolbox

description: Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the “4DNvestigator”, a user-friendly network based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales. <b>Availability</b>: https://github.com/lindsly/4DNvestigator
DOI: 10.6084/m9.figshare.7547729.v1
title: MOESM5 of Effects of amino acids on the lignocellulose degradation by Aspergillus fumigatus Z5: insights into performance, transcriptional, and proteomic profiles

description: Additional file 5: Dataset S4. Proteins of different families associated with cellulose degradation identified both in the proteome and transcriptome.
DOI: 10.6084/m9.figshare.20130907
title: Additional file 3 of Small extracellular vesicles derived from dermal fibroblasts promote fibroblast activity and skin development through carrying miR-218 and ITGBL1

description: Additional file 3: Dataset S1.The total miRNAs in CH-SEVs and LW-SEVs. Dataset S2. The differential miRNAs between CH-SEVs and LW-SEVs. Dataset S3.The total proteins in CH-SEVs and LW-SEVs. Dataset S4.The differential proteins between CH-SEVs and LW-SEVs.
DOI: 10.6084/m9.figshare.20131181
title: Additional file 6 of Safety and efficiency of stem cell therapy for COVID-19: a systematic review and meta-analysis

description: Additional file 6. All Adverse Events in Involved Studies. All adverse events (AEs), AEs related to treatment and numbers of patients with AEs reported in involved studies between experimental and control groups.
DOI: 10.25549/pmc-ouc1sto1797438
title: Polish Music Center Manuscript Collection
DOI: 10.6084/m9.figshare.10566794
title: Additional file 4: of Long noncoding RNA 00976 promotes pancreatic cancer progression through OTUD7B by sponging miR-137 involving EGFR/MAPK pathway

description: Table S2. Mass spectrometry of Immunoprecipitation proteins interacting with OTUD7B. (XLSX 935 kb)
DOI: 10.6084/m9.figshare.10566794.v1
title: Additional file 4: of Long noncoding RNA 00976 promotes pancreatic cancer progression through OTUD7B by sponging miR-137 involving EGFR/MAPK pathway

description: Table S2. Mass spectrometry of Immunoprecipitation proteins interacting with OTUD7B. (XLSX 935 kb)
DOI: 10.6084/m9.figshare.20130914
title: Additional file 12 of Single-cell RNA-seq reveals the genesis and heterogeneity of tumor microenvironment in pancreatic undifferentiated carcinoma with osteoclast-like giant-cells

description: Additional file 12: Table S4. DEGs of clusters of ductal type I subclusters at the resolution of 0.1.
DOI: 10.6084/m9.figshare.20130920
title: Additional file 14 of Single-cell RNA-seq reveals the genesis and heterogeneity of tumor microenvironment in pancreatic undifferentiated carcinoma with osteoclast-like giant-cells

description: Additional file 14: Table S6. gesGO analysis of cluster3 in figure 3.
DOI: 10.6084/m9.figshare.20130941
title: Additional file 20 of Single-cell RNA-seq reveals the genesis and heterogeneity of tumor microenvironment in pancreatic undifferentiated carcinoma with osteoclast-like giant-cells

description: Additional file 20: Table S12. GO BP analysis of beam markers.
DOI: 10.7910/dvn/vxpeht/q8rnbc
title: FurthreTest_nego_round.do

description: :unav
DOI: 10.7910/dvn/vxpeht/tk8bys
title: FurthreTest_regime.do

description: :unav
DOI: 10.7910/dvn/vxpeht/w2hdbx
title: FurthreTest_hetero.do

description: :unav
DOI: 10.18739/a29g5gd39
title: Contribution of the Greenland Ice Sheet to sea-level over the next millennium using Large Ensemble Simulations, spatial time series, 2008-3007

description: The Greenland Ice Sheet holds around 7.2 meters of sea-level equivalent. In recent decades rising atmosphere and ocean temperatures have led to an acceleration in mass loss, adding an average of about 0.5 millimeters per year to global mean sea-level between 1991 and 2015. Current ice margin recession in Greenland is led by the retreat of outlet glaciers, the large rivers of ice ending in narrow fjords that drain the ice sheet interior. Recent progress in measuring ice thickness is enabling models to reproduce the complex flow patterns found in outlet glaciers, a key step towards realistic projections. Here we pair an outlet glacier resolving ice sheet model with a comprehensive uncertainty quantification to estimate Greenland's contribution to sea-level over the next millennium under different climate forcings. We find that Greenland could contribute 5-33 centimeters to sea-level by 2100 and 11-155 centimeters by 2200, with discharge from outlet glaciers contributing 6-45% of the total mass loss. Our analysis shows that uncertainties in projecting mass loss are dominated by uncertainties in climate scenarios and surface processes, followed by ice dynamics, whereas uncertainties in ocean conditions play a minor role, particularly in the long term. We project that Greenland will very likely become ice-free within a millennium without significant reductions in greenhouse gas emissions. This dataset compilation contains the simulations for the manuscript "Contribution of the Greenland Ice Sheet to sea-level over the next millennium" prepared with the Parallel Ice Sheet Model (PISM). This dataset provides the likelihood of a pixel being ice covered at the year 3007 for the RCPs (Representative Concentration Pathways) 2.6, 4.5, and 8.5 for LES (Large Ensemble Simulations).