cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.10735643
title: Supplementary Material for: Efficacy of the Spiration Valve System in Patients with Severe Heterogeneous Emphysema: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Spiration Valve System (SVS) is an alternative for patients with severe heterogeneous emphysema; however, data about efficacy from randomized controlled trials (RCT) are unclear. <b><i>Objectives:</i></b> To explore both efficacy and safety of SVS in patients with severe emphysema and hyperinflation. <b><i>Methods:</i></b> We included PubMed, EMBASE, Coch­rane database. All searches were performed until August 2019. Only RCTs were included for analysis. Risk of bias was assessed using Cochrane risk of bias tool. A meta-analysis evaluated change in forced expiratory volume in 1 s (FEV<sub>1</sub>), 6-min walking test (6MWT), residual volume, modified medical research council (mMRC) and Saint George respiratory questionnaire (SGRQ), all-cause mortality, risk of pneumothorax, and risk of acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Quality of the evidence was rated using GRADE approach. <b><i>Results:</i></b> Four RCTs including 629 subjects were included. SVS showed an overall change of 0.03 L (–0.07 to 0.13, <i>I</i><sup>2</sup> = 90%) in the in FEV<sub>1</sub> (L) and a 2.03% (–2.50 to 6.57, <i>I</i><sup>2</sup> = 96%) in the predicted FEV<sub>1</sub> (%) compared to baseline; however, studies without collateral ventilation (CV) showed an improvement of 0.12 L (95% CI 0.09–0.015, <i>I</i><sup>2</sup> = 0%), This subgroup also reported better results in SGRQ –12.27 points (95% CI –15.84 to –8.70, <i>I</i><sup>2</sup> = 0%) and mMRC –0.54 (95% CI –0.74 to –0.33, <i>I</i><sup>2</sup> = 0%). We found no benefit in 6MWT mean difference = 4.56 m (95% CI –21.88 to 31.00, <i>I</i><sup>2</sup> = 73%). Relative risk of mortality was 2.54 (95% CI 0.81–7.96, <i>I</i><sup>2</sup> = 0%), for pneumothorax 3.3 (95% CI 0.61–18.12, <i>I</i><sup>2</sup> = 0%) and AECOPD 1.68 (95% CI 1.04–2.70, <i>I</i><sup>2</sup> = 0%). <b><i>Conclusion:</i></b> In patients with severe heterogeneous emphysema and hyperinflation without CV, SVS is an alternative that showed an improvement in pulmonary function, quality of life, and dyspnea score with an acceptable risk profile.
DOI: 10.6084/m9.figshare.10735499
title: Supplementary Material for: Active Cancer and Elevated D-Dimer Are Risk Factors for In-Hospital Ischemic Stroke

description: <b><i>Background and Purpose:</i></b> Little attention has been paid to the pathogenesis of in-hospital stroke, despite poor outcomes and a longer time from stroke onset to treatment. We studied the pathophysiology and biomarkers for detecting patients who progress to in-hospital ischemic stroke (IHS). <b><i>Methods:</i></b> Seventy-nine patients with IHS were sequentially recruited in the period 2011–2017. Their characteristics, care, and outcomes were compared with 933 patients who had an out-of-hospital ischemic stroke (OHS) using a prospectively collected database of the Tokushima University Stroke Registry. <b><i>Results:</i></b> Active cancer and coronary artery disease were more prevalent in patients with IHS than in those with OHS (53.2 and 27.8% vs. 2.0 and 10.9%, respectively; <i>p</i> &lt; 0.001), the median onset-to-evaluation time was longer (300 vs. 240 min; <i>p</i> = 0.015), and the undetermined etiology was significantly higher (36.7 vs. 2.4%; <i>p</i> &lt; 0.001). Although there was no significant difference in stroke severity at onset between the groups, patients with IHS had higher modified Rankin Scale (mRS) scores (3–6) at discharge (67.1 vs. 50.3%; <i>p</i> = 0.004) and rates of death during hospitalization (16.5 vs. 2.9%; <i>p</i> &lt; 0.001). D-dimer (5.8 vs. 0.8 µg/mL; <i>p</i> &lt; 0.001) and fibrinogen (532 vs. 430 mg/dL; <i>p</i> = 0.014) plasma levels at the time of onset were significantly higher in patients with IHS after propensity score matching. Multivariate logistic regression analysis revealed that active cancer (odds ratio [OR] 2.30; 95% confidence interval [CI] 1.26–4.20), prestroke mRS scores 3–5 (OR 6.78; 95% CI 3.96–11.61), female sex (OR 1.57; 95% CI 1.19–2.08), and age ≥75 years (OR 2.36; 95% CI 1.80–3.08) were associated with poor outcomes. <b><i>Conclusions:</i></b> Patients with IHS had poorer outcomes than those with OHS because of a higher prevalence of active cancer and functional dependence before stroke onset. Elevated plasma levels of D-dimer and fibrinogen, especially with active cancer, can help identify patients who are at a higher risk of progression to IHS.
DOI: 10.6084/m9.figshare.10735643.v1
title: Supplementary Material for: Efficacy of the Spiration Valve System in Patients with Severe Heterogeneous Emphysema: A Systematic Review and Meta-Analysis

description: <b><i>Background:</i></b> Spiration Valve System (SVS) is an alternative for patients with severe heterogeneous emphysema; however, data about efficacy from randomized controlled trials (RCT) are unclear. <b><i>Objectives:</i></b> To explore both efficacy and safety of SVS in patients with severe emphysema and hyperinflation. <b><i>Methods:</i></b> We included PubMed, EMBASE, Coch­rane database. All searches were performed until August 2019. Only RCTs were included for analysis. Risk of bias was assessed using Cochrane risk of bias tool. A meta-analysis evaluated change in forced expiratory volume in 1 s (FEV<sub>1</sub>), 6-min walking test (6MWT), residual volume, modified medical research council (mMRC) and Saint George respiratory questionnaire (SGRQ), all-cause mortality, risk of pneumothorax, and risk of acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Quality of the evidence was rated using GRADE approach. <b><i>Results:</i></b> Four RCTs including 629 subjects were included. SVS showed an overall change of 0.03 L (–0.07 to 0.13, <i>I</i><sup>2</sup> = 90%) in the in FEV<sub>1</sub> (L) and a 2.03% (–2.50 to 6.57, <i>I</i><sup>2</sup> = 96%) in the predicted FEV<sub>1</sub> (%) compared to baseline; however, studies without collateral ventilation (CV) showed an improvement of 0.12 L (95% CI 0.09–0.015, <i>I</i><sup>2</sup> = 0%), This subgroup also reported better results in SGRQ –12.27 points (95% CI –15.84 to –8.70, <i>I</i><sup>2</sup> = 0%) and mMRC –0.54 (95% CI –0.74 to –0.33, <i>I</i><sup>2</sup> = 0%). We found no benefit in 6MWT mean difference = 4.56 m (95% CI –21.88 to 31.00, <i>I</i><sup>2</sup> = 73%). Relative risk of mortality was 2.54 (95% CI 0.81–7.96, <i>I</i><sup>2</sup> = 0%), for pneumothorax 3.3 (95% CI 0.61–18.12, <i>I</i><sup>2</sup> = 0%) and AECOPD 1.68 (95% CI 1.04–2.70, <i>I</i><sup>2</sup> = 0%). <b><i>Conclusion:</i></b> In patients with severe heterogeneous emphysema and hyperinflation without CV, SVS is an alternative that showed an improvement in pulmonary function, quality of life, and dyspnea score with an acceptable risk profile.
DOI: 10.6084/m9.figshare.10733996
title: Pleural mesothelioma and lung cancer: the role of asbestos exposure and genetic variants in selected iron metabolism and inflammation genes

description: Two of the major cancerous diseases associated with asbestos exposure are malignant pleural mesothelioma (MPM) and lung cancer (LC). In addition to asbestos exposure, genetic factors have been suggested to be associated with asbestos-related carcinogenesis and lung genotoxicity. While genetic factors involved in the susceptibility to MPM were reported, to date the influence of individual genetic variations on asbestos-related lung cancer risk is still poorly understood. Since inflammation and disruption of iron (Fe) homeostasis are hallmarks of asbestos exposure affecting the pulmonary tissue, this study aimed at investigating the association between Fe-metabolism and inflammasome gene variants and susceptibility to develop LC or MPM, by comparing an asbestos-exposed population affected by LC with an “asbestos-resistant exposed population”. A retrospective approach similar to our previous autopsy-based pilot study was employed in a novel cohort of autoptic samples, thus giving us the possibility to corroborate previous findings obtained on MPM by repeating the analysis in a novel cohort of autoptic samples. The protective role of <i>HEPH</i> coding SNP was further confirmed. In addition, the two non-coding SNPs, either in <i>FTH1</i> or in <i>TF</i>, emerged to exert a similar protective role in a new cohort of LC exposed individuals from the same geographic area of MPM subjects. No association was found between <i>NLRP1</i> and <i>NLRP3</i> polymorphisms with susceptibility to develop MPM and LC. Further research into a specific MPM and LC “genetic signature” may be needed to broaden our knowledge of the genetic landscape attributed to result in MPM and LC.
DOI: 10.6084/m9.figshare.10733996.v1
title: Pleural mesothelioma and lung cancer: the role of asbestos exposure and genetic variants in selected iron metabolism and inflammation genes

description: Two of the major cancerous diseases associated with asbestos exposure are malignant pleural mesothelioma (MPM) and lung cancer (LC). In addition to asbestos exposure, genetic factors have been suggested to be associated with asbestos-related carcinogenesis and lung genotoxicity. While genetic factors involved in the susceptibility to MPM were reported, to date the influence of individual genetic variations on asbestos-related lung cancer risk is still poorly understood. Since inflammation and disruption of iron (Fe) homeostasis are hallmarks of asbestos exposure affecting the pulmonary tissue, this study aimed at investigating the association between Fe-metabolism and inflammasome gene variants and susceptibility to develop LC or MPM, by comparing an asbestos-exposed population affected by LC with an “asbestos-resistant exposed population”. A retrospective approach similar to our previous autopsy-based pilot study was employed in a novel cohort of autoptic samples, thus giving us the possibility to corroborate previous findings obtained on MPM by repeating the analysis in a novel cohort of autoptic samples. The protective role of <i>HEPH</i> coding SNP was further confirmed. In addition, the two non-coding SNPs, either in <i>FTH1</i> or in <i>TF</i>, emerged to exert a similar protective role in a new cohort of LC exposed individuals from the same geographic area of MPM subjects. No association was found between <i>NLRP1</i> and <i>NLRP3</i> polymorphisms with susceptibility to develop MPM and LC. Further research into a specific MPM and LC “genetic signature” may be needed to broaden our knowledge of the genetic landscape attributed to result in MPM and LC.
DOI: 10.6084/m9.figshare.10732871
title: Data and code.zip

description: Data and code used in IJGIS paper
DOI: 10.6084/m9.figshare.10732871.v2
title: Data and code.zip

description: Data and code used in IJGIS paper
DOI: 10.6084/m9.figshare.10732871.v1
title: Data and code.zip

description: Data and code used in IJGIS paper
DOI: 10.6084/m9.figshare.10732415
title: Force curves raw data

description: Force curves recorded on live cells (microglia and fibroblasts) or PAA beads on elastic substrates. Data was recorded using a JPK CellHesion200 AFM. Force curve raw data is stored in JPK file format and as text file. Folder names are numbered by experiment day, subfolders denote approximate substrate shear moduli. For each cell/bead, at least three forces curves were recordded at the cell/bead center, one force curve was recorded on the substrate next to the cell/bead for height and stiffness reference, and an optical phase contrast image was taken.
DOI: 10.11583/dtu.10732412
title: Consolidated Challenges Regarding Execution of Portfolio Rationalization Projects in an Engineer-to-Order Context

description: Consolidated collection of literature and case challenges from portfolio rationalization projects. The authors invite fellows to extend with more challenges and expand with more case studies.
DOI: 10.6084/m9.figshare.10732349
title: Fig. 3

description: <b>Figure 3</b>. Velocity-weakening zone length (a) as a function of normalized time in three fluid injection experiments, and (b) evolves before and after fault slip in the E1 experiment and corresponding fluid pressure variation in the injection borehole.
DOI: 10.6084/m9.figshare.10732352
title: Fig. S1

description: <b>Figure S1</b> Validation of numerical model in comparison to experimental data and fluid pressure contour on the fracture at the end of fluid injection (inset).
DOI: 10.6084/m9.figshare.10732352.v1
title: Fig. S1

description: <b>Figure S1</b> Validation of numerical model in comparison to experimental data and fluid pressure contour on the fracture at the end of fluid injection (inset).
DOI: 10.6084/m9.figshare.10732346
title: Fig. 2

description: <b>Figure 2</b>. (b) typical friction coefficient versus slip displacement curve under 30.0 MPa normal stress, and (c) friction rate parameter (<i>a-b</i>) as a function of the ratio of fluid pressure to normal stress.
DOI: 10.6084/m9.figshare.10732349.v1
title: Fig. 3

description: <b>Figure 3</b>. Velocity-weakening zone length (a) as a function of normalized time in three fluid injection experiments, and (b) evolves before and after fault slip in the E1 experiment and corresponding fluid pressure variation in the injection borehole.
DOI: 10.6084/m9.figshare.10732340
title: Fig. 1

description: <b>Figure 1</b>. (b) injection and monitoring pressures and slip displacement during the fluid injection experiment with 0.01 mL/min injection rate, and (c) time-dependent fluid pressure distribution as a function of distance to the injection borehole along the major axis of the fault.
DOI: 10.6084/m9.figshare.10732346.v1
title: Fig. 2

description: <b>Figure 2</b>. (b) typical friction coefficient versus slip displacement curve under 30.0 MPa normal stress, and (c) friction rate parameter (<i>a-b</i>) as a function of the ratio of fluid pressure to normal stress.
DOI: 10.6084/m9.figshare.10732340.v1
title: Fig. 1

description: <b>Figure 1</b>. (b) injection and monitoring pressures and slip displacement during the fluid injection experiment with 0.01 mL/min injection rate, and (c) time-dependent fluid pressure distribution as a function of distance to the injection borehole along the major axis of the fault.
DOI: 10.6084/m9.figshare.10731632
title: Data of Kim et al., 2019 (JGR-atmosphere)

description: Data set of Kim et al., 2019
DOI: 10.6084/m9.figshare.10731632.v1
title: Data of Kim et al., 2019 (JGR-atmosphere)

description: Data set of Kim et al., 2019
DOI: 10.6084/m9.figshare.10731425
title: MOESM1 of Prevalence of pathogens in ticks collected from humans through citizen science in Belgium

description: Additional file 1: Table S1. Dataset of qPCR results and DNA sequences.
DOI: 10.6084/m9.figshare.10731422
title: MOESM1 of Secondary care usage and characteristics of hospital inpatients referred to a UK homeless health team: a retrospective service evaluation

description: Additional file 1. Data extraction template. Blank data extraction document for recording data extracted per patient.
DOI: 10.6084/m9.figshare.10731422.v1
title: MOESM1 of Secondary care usage and characteristics of hospital inpatients referred to a UK homeless health team: a retrospective service evaluation

description: Additional file 1. Data extraction template. Blank data extraction document for recording data extracted per patient.
DOI: 10.6084/m9.figshare.10731425.v1
title: MOESM1 of Prevalence of pathogens in ticks collected from humans through citizen science in Belgium

description: Additional file 1: Table S1. Dataset of qPCR results and DNA sequences.
DOI: 10.6084/m9.figshare.10731380
title: MOESM6 of Distinct migratory pattern of naive and effector T cells through the blood–CSF barrier following Echovirus 30 infection

description: Additional file 6. Migration of T cells following E-30 has no impact on the paracellular dextran flux of HIBCPP cells. The table is showing all - p-values.
DOI: 10.6084/m9.figshare.10731374
title: MOESM5 of Distinct migratory pattern of naive and effector T cells through the blood–CSF barrier following Echovirus 30 infection

description: Additional file 5. Migration of T cells following E-30 has no impact on TEER of HIBCPP cells. The table is showing all - p-values.
DOI: 10.6084/m9.figshare.10731380.v1
title: MOESM6 of Distinct migratory pattern of naive and effector T cells through the blood–CSF barrier following Echovirus 30 infection

description: Additional file 6. Migration of T cells following E-30 has no impact on the paracellular dextran flux of HIBCPP cells. The table is showing all - p-values.
DOI: 10.6084/m9.figshare.10731374.v1
title: MOESM5 of Distinct migratory pattern of naive and effector T cells through the blood–CSF barrier following Echovirus 30 infection

description: Additional file 5. Migration of T cells following E-30 has no impact on TEER of HIBCPP cells. The table is showing all - p-values.
DOI: 10.6084/m9.figshare.10731347
title: MOESM2 of EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

description: Additional file 2: Supplementary Table S1-S5.
DOI: 10.6084/m9.figshare.10731347.v1
title: MOESM2 of EpiMethylTag: simultaneous detection of ATAC-seq or ChIP-seq signals with DNA methylation

description: Additional file 2: Supplementary Table S1-S5.
DOI: 10.6084/m9.figshare.10731326
title: MOESM3 of Randomized SMILES strings improve the quality of molecular generative models

description: Additional file 3. Supplementary tables.
DOI: 10.6084/m9.figshare.10731326.v1
title: MOESM3 of Randomized SMILES strings improve the quality of molecular generative models

description: Additional file 3. Supplementary tables.
DOI: 10.25345/c5v178
title: MassIVE MSV000086019 - GNPS CCL unifi mgf test 20200826
title: CCL compounds. Data collected using IMS under positive ionization mode. Data converted using Unifi.
DOI: 10.6084/m9.figshare.10731218
title: MOESM1 of Effects of school-based physical activity on mathematics performance in children: a systematic review

description: Additional file 1: Systematic search strategy.
DOI: 10.6084/m9.figshare.10731218.v1
title: MOESM1 of Effects of school-based physical activity on mathematics performance in children: a systematic review

description: Additional file 1: Systematic search strategy.
DOI: 10.6084/m9.figshare.10731206
title: MOESM3 of Wrangling environmental exposure data: guidance for getting the best information from your laboratory measurements

description: Additional file 3: Example of report formatting request to send to the lab.
DOI: 10.6084/m9.figshare.10731206.v1
title: MOESM3 of Wrangling environmental exposure data: guidance for getting the best information from your laboratory measurements

description: Additional file 3: Example of report formatting request to send to the lab.
DOI: 10.6084/m9.figshare.10731137
title: MOESM7 of Evaluation of honey-baited FTA cards in combination with different mosquito traps in an area of low arbovirus prevalence

description: Additional file 5: Table S5. Raw data set.
DOI: 10.6084/m9.figshare.10731137.v1
title: MOESM7 of Evaluation of honey-baited FTA cards in combination with different mosquito traps in an area of low arbovirus prevalence

description: Additional file 5: Table S5. Raw data set.
DOI: 10.6084/m9.figshare.10731095
title: MOESM3 of Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

description: Additional file 3 Data from Mouse Infections, and ZINB Test Example (zip file) - Experimental data for the mouse experiment in Section 3.2 (.wig files with transposon insertion counts at TA sites), along with Instructions (README.docx) on how to do the ZINB analysis in TRANSIT (commands and output files).
DOI: 10.6084/m9.figshare.10731086
title: MOESM2 of Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

description: Additional file 2 Supplemental Table 2 - ZINB output file containing results for Section 3.4 on comparison of a TnSeq library for M. tuberculosis H37Rv grown in presence of five antibiotics, isoniazid (INH), rifampicin (RIF), ethambutol (EMB), meropenem (MER), and vancomycin (VAN).
DOI: 10.6084/m9.figshare.10731086.v1
title: MOESM2 of Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

description: Additional file 2 Supplemental Table 2 - ZINB output file containing results for Section 3.4 on comparison of a TnSeq library for M. tuberculosis H37Rv grown in presence of five antibiotics, isoniazid (INH), rifampicin (RIF), ethambutol (EMB), meropenem (MER), and vancomycin (VAN).
DOI: 10.6084/m9.figshare.10731095.v1
title: MOESM3 of Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

description: Additional file 3 Data from Mouse Infections, and ZINB Test Example (zip file) - Experimental data for the mouse experiment in Section 3.2 (.wig files with transposon insertion counts at TA sites), along with Instructions (README.docx) on how to do the ZINB analysis in TRANSIT (commands and output files).
DOI: 10.6084/m9.figshare.10731080
title: MOESM1 of Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

description: Additional file 1 Supplemental Table 1 - ZINB output file (spreadsheet, tab-separated format) containing results from Section 3.2 on comparison of a TnSeq library for M. tuberculosis H37Rv grown in-vitro versus in C57BL/6 mice. For each ORF in the genome, an analysis of the mean, NZ-mean, and saturation in each condition is given, along with p-value and adjusted p-value. Significantly varying genes are those with padj&lt;0.05.
DOI: 10.6084/m9.figshare.10731077
title: MOESM1 of Strain imaging to assess early effects of successful percutaneous balloon mitral valvotomy on left atrium mechanics

description: Additional file 1: Raw data from patients with mitral stenosis before and balloon mitral valvotomy and in controls.
DOI: 10.6084/m9.figshare.10731080.v1
title: MOESM1 of Statistical analysis of variability in TnSeq data across conditions using zero-inflated negative binomial regression

description: Additional file 1 Supplemental Table 1 - ZINB output file (spreadsheet, tab-separated format) containing results from Section 3.2 on comparison of a TnSeq library for M. tuberculosis H37Rv grown in-vitro versus in C57BL/6 mice. For each ORF in the genome, an analysis of the mean, NZ-mean, and saturation in each condition is given, along with p-value and adjusted p-value. Significantly varying genes are those with padj&lt;0.05.
DOI: 10.6084/m9.figshare.10731077.v1
title: MOESM1 of Strain imaging to assess early effects of successful percutaneous balloon mitral valvotomy on left atrium mechanics

description: Additional file 1: Raw data from patients with mitral stenosis before and balloon mitral valvotomy and in controls.
DOI: 10.6084/m9.figshare.10731050
title: MOESM1 of Co-circulation of the two influenza B lineages during 13 consecutive influenza surveillance seasons in Italy, 2004–2017

description: Additional file 1: Table S1. GISAID accession numbers (AN) for hemagglutinin (HA) of influenza B viruses generated in this study (*) and used for the phylogenetic analysis, along with other Italian sequences retrieved from GISAID or NCBI database and reference and WHO vaccine strains (in bold).
DOI: 10.6084/m9.figshare.10731050.v1
title: MOESM1 of Co-circulation of the two influenza B lineages during 13 consecutive influenza surveillance seasons in Italy, 2004–2017

description: Additional file 1: Table S1. GISAID accession numbers (AN) for hemagglutinin (HA) of influenza B viruses generated in this study (*) and used for the phylogenetic analysis, along with other Italian sequences retrieved from GISAID or NCBI database and reference and WHO vaccine strains (in bold).