cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12452066
title: Additional file 4 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 4: Table S3. List of Key GBM genes (n = 78), pooled from SweGBM-1 FMGs and TCGA-GBM SMGs.
DOI: 10.6084/m9.figshare.12452060.v1
title: Additional file 3 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 3: Table S2. Intersection of alterations in SweGBM-1 FMGs with TCGA-GBM dataset and with pan-cancer databases of COSMIC, cBioPortal and CancerHotspots.
DOI: 10.6084/m9.figshare.12452051
title: Additional file 2 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 2: Table S1. TCGA top 20 GBM genes that overlap with SweGBM-1 cohort.
DOI: 10.6084/m9.figshare.12452066.v1
title: Additional file 4 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 4: Table S3. List of Key GBM genes (n = 78), pooled from SweGBM-1 FMGs and TCGA-GBM SMGs.
DOI: 10.6084/m9.figshare.12452051.v1
title: Additional file 2 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 2: Table S1. TCGA top 20 GBM genes that overlap with SweGBM-1 cohort.
DOI: 10.6084/m9.figshare.12452033
title: Additional file 11 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 11: Table S10. Annotation of the NCCMs associated with the SLC25A21, MIPOL1, FOXA1, and TTC6 genes based on data from the ENCODE portal and the UCSC Browser databases.
DOI: 10.6084/m9.figshare.12452030
title: Additional file 10 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 10: Table S9. Annotation of the NCCMs associated with the DLX5 and DLX6 genes based on data from the ENCODE portal and the UCSC Browser databases.
DOI: 10.6084/m9.figshare.12452033.v1
title: Additional file 11 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 11: Table S10. Annotation of the NCCMs associated with the SLC25A21, MIPOL1, FOXA1, and TTC6 genes based on data from the ENCODE portal and the UCSC Browser databases.
DOI: 10.6084/m9.figshare.12452030.v1
title: Additional file 10 of Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes

description: Additional file 10: Table S9. Annotation of the NCCMs associated with the DLX5 and DLX6 genes based on data from the ENCODE portal and the UCSC Browser databases.
DOI: 10.6084/m9.figshare.12451937
title: Supplementary Material for: Temporary Right Middle Lobe Occlusion with a Blocking Device to Enable Collateral Ventilation Measurement of the Right Major Fissure

description: <b><i>Background:</i></b> Absence of interlobar collateral ventilation is essential to achieve lobar volume reduction after endobronchial valve (EBV) treatment and can be assessed using the Chartis measurement. However, especially in lower lobe measurements, Chartis can be complicated by the “no-flow phenomenon”, during which a sudden cessation of flow is observed, leading to an unreliable measurement. If this phenomenon occurs in the right lower lobe, when measuring collateral flow over the right major fissure, the entrance to the right middle lobe should be occluded, and the Chartis balloon should be placed in the right upper lobe. Both Watanabe spigots and balloon catheters can be used to achieve occlusion. <b><i>Objective:</i></b> Our aim was to demonstrate that right middle lobe occlusion with a blocking device is helpful in obtaining a reliable Chartis outcome in case of the no-flow phenomenon in the right lower lobe. <b><i>Methods:</i></b> We performed a retrospective analysis of patients scheduled for EBV treatment in an EBV registry between September 2016 and September 2019. <b><i>Results:</i></b> We included 15 patients with severe emphysema (median age 63 years [range 47–73], 73% female, and FEV<sub>1</sub> 24% [range 19–36] of predicted), who required temporary middle lobe occlusion (12 Watanabe spigot, 3 balloon catheter). After occlusion, a reliable Chartis outcome was obtained in all patients. <b><i>Conclusion:</i></b> Temporary middle lobe occlusion using a blocking device is helpful in obtaining a reliable Chartis outcome in case of a right lower lobe no-flow phenomenon.
DOI: 10.6084/m9.figshare.12451904
title: Supplementary Material for: Assessing the Predictive Performance of Probabilistic Caries Risk Assessment Models: The Importance of Calibration

description: Probabilistic caries risk assessment models (P-CRA), such as the Cariogram, are promising tools to planning treatments in order to control and prevent caries. The usefulness of these models for informing patients and medical decision-making depends on 2 properties known as discrimination and calibration. Current common assessment of P-CRA models, however, ignores calibration, and this can be misleading. The aim of this paper was to provide tools for a proper assessment of calibration of the P-CRA models and improve calibration when lacking. A combination of standard calibration tools (calibration plot, calibration in-the-large, and calibration slope) and 3 novel measures of calibration (the Calibration Index and 2 related metrics, E50 and E90) are proposed to evaluate if a P-CRA model is well calibrated. Moreover, an approach was proposed and validated using data from a previous follow-up study performed on children evaluated by means of a reduced Cariogram model; Platt scaling and isotonic regression were applied showing a lack of calibration. The use of the Cariogram overestimates the actual risk of new caries for forecast probabilities &lt;0.5 and underestimates the risk for forecast probabilities &gt;0.6. Both Platt scaling and isotonic regression were able to significantly improve the calibration of the reduced Cariogram model, preserving its discrimination properties. The average specificity and sensitivity for both Platt scaling and isotonic regression using the cut-off point <i>p</i>= 0.5 were &gt;83 and their sum well exceeded 160. The benefits of the proposed calibration methods are promising, but further research in this field is required.
DOI: 10.6084/m9.figshare.12451904.v1
title: Supplementary Material for: Assessing the Predictive Performance of Probabilistic Caries Risk Assessment Models: The Importance of Calibration

description: Probabilistic caries risk assessment models (P-CRA), such as the Cariogram, are promising tools to planning treatments in order to control and prevent caries. The usefulness of these models for informing patients and medical decision-making depends on 2 properties known as discrimination and calibration. Current common assessment of P-CRA models, however, ignores calibration, and this can be misleading. The aim of this paper was to provide tools for a proper assessment of calibration of the P-CRA models and improve calibration when lacking. A combination of standard calibration tools (calibration plot, calibration in-the-large, and calibration slope) and 3 novel measures of calibration (the Calibration Index and 2 related metrics, E50 and E90) are proposed to evaluate if a P-CRA model is well calibrated. Moreover, an approach was proposed and validated using data from a previous follow-up study performed on children evaluated by means of a reduced Cariogram model; Platt scaling and isotonic regression were applied showing a lack of calibration. The use of the Cariogram overestimates the actual risk of new caries for forecast probabilities &lt;0.5 and underestimates the risk for forecast probabilities &gt;0.6. Both Platt scaling and isotonic regression were able to significantly improve the calibration of the reduced Cariogram model, preserving its discrimination properties. The average specificity and sensitivity for both Platt scaling and isotonic regression using the cut-off point <i>p</i>= 0.5 were &gt;83 and their sum well exceeded 160. The benefits of the proposed calibration methods are promising, but further research in this field is required.
DOI: 10.6084/m9.figshare.12451820
title: CELF2 stabilize FAM198B in ovarian cancer

description: 1.Transcripts significantly differential expressed between 10 ovarian cancer tissues and 8 normal ovarian tissues;2.The complete gene list associated to CELF2 protein by high-throughput RNA immunoprecipitation sequencing in A2780 cells;3.Genes differentially expressed in CELF2-overexpressed SK-OV-3 cells compared with NC cells by RNA-seq
DOI: 10.6084/m9.figshare.12451790
title: Supplementary Material for: Antenatal Magnesium Sulfate and Preeclampsia Differentially Affect Neonatal Cerebral Oxygenation

description: <b><i>Introduction:</i></b> Magnesium sulfate (MgSO<sub>4</sub>) is frequently administered for maternal and fetal neuroprotection in preeclampsia (PE) and imminent preterm birth, respectively. <b><i>Objective:</i></b> To assess whether MgSO<sub>4</sub> affects neonatal cerebral oxygenation, blood flow, and cerebral autoregulation (CAR) during the first postnatal days independently from PE. <b><i>Methods:</i></b> 148 neonates &lt;32 weeks gestational age were included. Cerebral fractional tissue oxygen extraction (cFTOE) was extracted from a daily 2-h period, during which peak systolic blood flow velocity (PSV) and resistance index (RI) of the pericallosal artery were obtained. The percent time of impaired CAR (correlation coefficient between mean arterial blood pressure and cerebral oxygen saturation &gt;0.5) was determined. Linear mixed models were applied. <b><i>Results:</i></b> MgSO<sub>4</sub> exposure was recorded in 77 neonates. Twenty-nine neonates were born following PE. MgSO<sub>4</sub> independently lowered cFTOE (B: –0.026, 95% CI: –0.050 to 0.002, <i>p</i> &lt; 0.05) but did not affect PSV and RI. PE was associated with a lower cFTOE (B: –0.041, 95% CI: –0.067 to –0.015, <i>p</i> &lt; 0.05) and a tendency towards both lower PSV (B: –4.285, 95% CI: –9.067 to 0.497, <i>p</i> &lt; 0.1) and more impaired CAR (B: 4.042, 95% CI: –0.028 to 8.112, <i>p</i> &lt; 0.1), which seemed to be strongly mediated by fetal brain sparing. MgSO<sub>4</sub> did not alter CAR. <b><i>Conclusions:</i></b> In contrast to fetal brain sparing in PE, MgSO<sub>4</sub> seems to lower cFTOE by lowering cerebral oxygen demands in preterm neonates without affecting the cerebrovasculature.
DOI: 10.6084/m9.figshare.12451820.v1
title: CELF2 stabilize FAM198B in ovarian cancer

description: 1.Transcripts significantly differential expressed between 10 ovarian cancer tissues and 8 normal ovarian tissues;2.The complete gene list associated to CELF2 protein by high-throughput RNA immunoprecipitation sequencing in A2780 cells;3.Genes differentially expressed in CELF2-overexpressed SK-OV-3 cells compared with NC cells by RNA-seq
DOI: 10.6084/m9.figshare.12451790.v1
title: Supplementary Material for: Antenatal Magnesium Sulfate and Preeclampsia Differentially Affect Neonatal Cerebral Oxygenation

description: <b><i>Introduction:</i></b> Magnesium sulfate (MgSO<sub>4</sub>) is frequently administered for maternal and fetal neuroprotection in preeclampsia (PE) and imminent preterm birth, respectively. <b><i>Objective:</i></b> To assess whether MgSO<sub>4</sub> affects neonatal cerebral oxygenation, blood flow, and cerebral autoregulation (CAR) during the first postnatal days independently from PE. <b><i>Methods:</i></b> 148 neonates &lt;32 weeks gestational age were included. Cerebral fractional tissue oxygen extraction (cFTOE) was extracted from a daily 2-h period, during which peak systolic blood flow velocity (PSV) and resistance index (RI) of the pericallosal artery were obtained. The percent time of impaired CAR (correlation coefficient between mean arterial blood pressure and cerebral oxygen saturation &gt;0.5) was determined. Linear mixed models were applied. <b><i>Results:</i></b> MgSO<sub>4</sub> exposure was recorded in 77 neonates. Twenty-nine neonates were born following PE. MgSO<sub>4</sub> independently lowered cFTOE (B: –0.026, 95% CI: –0.050 to 0.002, <i>p</i> &lt; 0.05) but did not affect PSV and RI. PE was associated with a lower cFTOE (B: –0.041, 95% CI: –0.067 to –0.015, <i>p</i> &lt; 0.05) and a tendency towards both lower PSV (B: –4.285, 95% CI: –9.067 to 0.497, <i>p</i> &lt; 0.1) and more impaired CAR (B: 4.042, 95% CI: –0.028 to 8.112, <i>p</i> &lt; 0.1), which seemed to be strongly mediated by fetal brain sparing. MgSO<sub>4</sub> did not alter CAR. <b><i>Conclusions:</i></b> In contrast to fetal brain sparing in PE, MgSO<sub>4</sub> seems to lower cFTOE by lowering cerebral oxygen demands in preterm neonates without affecting the cerebrovasculature.
DOI: 10.6084/m9.figshare.12451151
title: Metadata record for: A benchmark dataset of protein antigens for antigenicity measurement

description: This dataset contains key characteristics about the data described in the Data Descriptor A benchmark dataset of protein antigens for antigenicity measurement. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12451151.v1
title: Metadata record for: A benchmark dataset of protein antigens for antigenicity measurement

description: This dataset contains key characteristics about the data described in the Data Descriptor A benchmark dataset of protein antigens for antigenicity measurement. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br> <br> <br>
DOI: 10.6084/m9.figshare.12450986
title: Additional file 3 of Serum and fecal profiles of aromatic microbial metabolites reflect gut microbiota disruption in critically ill patients: a prospective observational pilot study

description: Additional file 3: Supplementary Table 1. - Clinical characteristics of the patients in the ACI and the CCI groups of patients. Supplementary Table 2. - Additional sample information: patient ID and time point (day of collection).
DOI: 10.6084/m9.figshare.12450986.v1
title: Additional file 3 of Serum and fecal profiles of aromatic microbial metabolites reflect gut microbiota disruption in critically ill patients: a prospective observational pilot study

description: Additional file 3: Supplementary Table 1. - Clinical characteristics of the patients in the ACI and the CCI groups of patients. Supplementary Table 2. - Additional sample information: patient ID and time point (day of collection).
DOI: 10.6084/m9.figshare.12450971
title: Additional file 1 of Hotspots of unimproved sources of drinking water in Ethiopia: mapping and spatial analysis of Ethiopia demographic and health survey Data 2016

description: Additional file 1. Significant spatial windows which contain primary and secondary clusters of unimproved sources of drinking water in Ethiopia, EDHS 2016. A cluster is statistically significant when its LLR is greater than the critical value, which is, for a significance level (Standard Monte Carlo Critical Values: 0.001: 11.90; 0.01: 10.32; 0.05: 8.72).
DOI: 10.6084/m9.figshare.12450971.v1
title: Additional file 1 of Hotspots of unimproved sources of drinking water in Ethiopia: mapping and spatial analysis of Ethiopia demographic and health survey Data 2016

description: Additional file 1. Significant spatial windows which contain primary and secondary clusters of unimproved sources of drinking water in Ethiopia, EDHS 2016. A cluster is statistically significant when its LLR is greater than the critical value, which is, for a significance level (Standard Monte Carlo Critical Values: 0.001: 11.90; 0.01: 10.32; 0.05: 8.72).
DOI: 10.6084/m9.figshare.12450851
title: Additional file 2 of Perceptions of barriers and levers of health-enhancing physical activity policies in mid-size French municipalities

description: Additional file 2.
DOI: 10.6084/m9.figshare.12450851.v1
title: Additional file 2 of Perceptions of barriers and levers of health-enhancing physical activity policies in mid-size French municipalities

description: Additional file 2.
DOI: 10.6084/m9.figshare.12450827
title: Additional file 6 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 6 New Eutrema salsugineum genome annotation containing XLOCs identified by Champigny et al. [25] and novel DLOCs identified in this study. File is set up in same column order as.gtf format.
DOI: 10.6084/m9.figshare.12450821
title: Additional file 5 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 5 GO enrichment of selected clusters.
DOI: 10.6084/m9.figshare.12450827.v1
title: Additional file 6 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 6 New Eutrema salsugineum genome annotation containing XLOCs identified by Champigny et al. [25] and novel DLOCs identified in this study. File is set up in same column order as.gtf format.
DOI: 10.6084/m9.figshare.12450821.v1
title: Additional file 5 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 5 GO enrichment of selected clusters.
DOI: 10.6084/m9.figshare.12450812
title: Additional file 4 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 4 DEG composition of all clusters.
DOI: 10.6084/m9.figshare.12450803
title: Additional file 3 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 3 Significant DEGs identified at all biologically relevant drought progression stages.
DOI: 10.6084/m9.figshare.12450812.v1
title: Additional file 4 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 4 DEG composition of all clusters.
DOI: 10.6084/m9.figshare.12450803.v1
title: Additional file 3 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 3 Significant DEGs identified at all biologically relevant drought progression stages.
DOI: 10.6084/m9.figshare.12450794
title: Additional file 2 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 2 List of predicted lncRNAs.
DOI: 10.6084/m9.figshare.12450794.v1
title: Additional file 2 of Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

description: Additional file 2 List of predicted lncRNAs.
DOI: 10.6084/m9.figshare.12450686
title: Additional file 1 of The clinical application of electrical impedance technology in the detection of malignant neoplasms: a systematic review

description: Additional file 1. Table S1. Detailed secondary outcomes of all studies.
DOI: 10.6084/m9.figshare.12450686.v1
title: Additional file 1 of The clinical application of electrical impedance technology in the detection of malignant neoplasms: a systematic review

description: Additional file 1. Table S1. Detailed secondary outcomes of all studies.
DOI: 10.6084/m9.figshare.12450665
title: Additional file 6 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 6: Table S5. Customized primers sequences used for real-time qPCR and gRNA sequences.
DOI: 10.6084/m9.figshare.12450665.v1
title: Additional file 6 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 6: Table S5. Customized primers sequences used for real-time qPCR and gRNA sequences.
DOI: 10.6084/m9.figshare.12450656
title: Additional file 5 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 5: Table S4. The analyzed loci in GWAS catalog and CardiogramplusC4D databases.
DOI: 10.6084/m9.figshare.12450656.v1
title: Additional file 5 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 5: Table S4. The analyzed loci in GWAS catalog and CardiogramplusC4D databases.
DOI: 10.6084/m9.figshare.12450647
title: Additional file 4 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 4: Table S3. The samples source and subject information.
DOI: 10.6084/m9.figshare.12450638
title: Additional file 3 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 3: Table S2. The candidate CAD associated genes with TCF21 binding, chromatin accessibility and chromosomal looping QTLs loci.
DOI: 10.6084/m9.figshare.12450647.v1
title: Additional file 4 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 4: Table S3. The samples source and subject information.
DOI: 10.6084/m9.figshare.12450629
title: Additional file 2 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 2: Table S1. Regressions of significant TCF21 binding QTLs, chromatin accessibility QTLs and chromosomal looping QTLs.
DOI: 10.6084/m9.figshare.12450638.v1
title: Additional file 3 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 3: Table S2. The candidate CAD associated genes with TCF21 binding, chromatin accessibility and chromosomal looping QTLs loci.
DOI: 10.6084/m9.figshare.12450629.v1
title: Additional file 2 of Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping

description: Additional file 2: Table S1. Regressions of significant TCF21 binding QTLs, chromatin accessibility QTLs and chromosomal looping QTLs.