cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.10592146
title: Patient-reported outcomes in the aging population of adults with congenital heart disease results from APPROACH-IS

description: Moons P, Luyckx K, Thomet C, Budts W, Enomoto J, Sluman MA, Yang HL, Jackson JL, Khairy P, Cook SC, Chidambarathanu S, Alday L, Oechslin E, Eriksen K, Dellborg M, Berghammer M, Johansson B, Mackie AS, Menahem S, Caruana M, Veldtman G, Soufi A, Fernandes SM, White K, Callus E, Kutty S, Kovacs AH; APPROACH-IS consortium. Patient-reported outcomes in the aging population of adults with congenital heart disease: results from APPROACH-IS. Eur J Cardiovasc Nurs. 2023 May 25;22(4):339-344. doi: 10.1093/eurjcn/zvac057. PMID: 35901014.

Abstract



The congenital heart disease (CHD) population now comprises an increasing number of older persons in their 6th decade of life and beyond. We cross-sectionally evaluated patient-reported outcomes (PROs) in persons with CHD aged 60 years or older, and contrasted these with PROs of younger patients aged 40-59 years and 18-39 years. Adjusted for demographic and medical characteristics, patients ≥60 years had a lower Physical Component Summary, higher Mental Component Summary, and lower anxiety (Hospital Anxiety and Depression Scale-Anxiety) scores than patients in the two younger categories. For satisfaction with life, older persons had a higher score than patients aged 40-59 years. Registration: ClinicalTrials.gov NCT02150603.
DOI: 10.5281/zenodo.10592100
title: Model-based spectral causality of cardiovascular variability interactions during head-down tilt

description: Porta A, Cairo B, Bari V, Gelpi F, De Maria B, Colombo R. Model-based spectral causality of cardiovascular variability interactions during head-down tilt. Physiol Meas. 2023 May 9;44(5). doi: 10.1088/1361-6579/acce1f. PMID: 37072006.

Abstract



Objective. Cardiovascular control mechanisms are commonly studied during baroreceptor unloading induced by head-up tilt. Conversely, the effect of a baroreceptor loading induced by head-down tilt (HDT) is less studied especially when the stimulus is of moderate intensity and using model-based spectral causality markers. Thus, this study computes model-based causality markers in the frequency domain derived via causal squared coherence and Geweke spectral causality approach from heart period (HP) and systolic arterial pressure (SAP) variability series.Approach. We recorded HP and SAP variability series in 12 healthy men (age: from 41 to 71 yrs, median: 57 yrs) during HDT at -25°. The approaches are compared by considering two different bivariate model structures, namely the autoregressive and dynamic adjustment models. Markers are computed in traditional frequency bands utilized in cardiovascular control analysis, namely the low frequency (LF, from 0.04 to 0.15 Hz) and high frequency (HF, from 0.15 to 0.4 Hz) bands.Main results. We found that: (i) the two spectral causality metrics are deterministically related but spectral causality markers exhibit different discriminative ability; (ii) HDT reduces the involvement of the baroreflex in regulating HP-SAP variability interactions in the LF band, while leaving unmodified the action of mechanical feedforward mechanisms in both LF and HF bands; (iii) this conclusion does not depend on the model structure.Significance. We conclude that HDT can be utilized to reduce the impact of baroreflex and to study the contribution of regulatory mechanisms different from baroreflex to the complexity of cardiovascular control in humans.
DOI: 10.5281/zenodo.10592101
title: Model-based spectral causality of cardiovascular variability interactions during head-down tilt

description: Porta A, Cairo B, Bari V, Gelpi F, De Maria B, Colombo R. Model-based spectral causality of cardiovascular variability interactions during head-down tilt. Physiol Meas. 2023 May 9;44(5). doi: 10.1088/1361-6579/acce1f. PMID: 37072006.

Abstract



Objective. Cardiovascular control mechanisms are commonly studied during baroreceptor unloading induced by head-up tilt. Conversely, the effect of a baroreceptor loading induced by head-down tilt (HDT) is less studied especially when the stimulus is of moderate intensity and using model-based spectral causality markers. Thus, this study computes model-based causality markers in the frequency domain derived via causal squared coherence and Geweke spectral causality approach from heart period (HP) and systolic arterial pressure (SAP) variability series.Approach. We recorded HP and SAP variability series in 12 healthy men (age: from 41 to 71 yrs, median: 57 yrs) during HDT at -25°. The approaches are compared by considering two different bivariate model structures, namely the autoregressive and dynamic adjustment models. Markers are computed in traditional frequency bands utilized in cardiovascular control analysis, namely the low frequency (LF, from 0.04 to 0.15 Hz) and high frequency (HF, from 0.15 to 0.4 Hz) bands.Main results. We found that: (i) the two spectral causality metrics are deterministically related but spectral causality markers exhibit different discriminative ability; (ii) HDT reduces the involvement of the baroreflex in regulating HP-SAP variability interactions in the LF band, while leaving unmodified the action of mechanical feedforward mechanisms in both LF and HF bands; (iii) this conclusion does not depend on the model structure.Significance. We conclude that HDT can be utilized to reduce the impact of baroreflex and to study the contribution of regulatory mechanisms different from baroreflex to the complexity of cardiovascular control in humans.
DOI: 10.5281/zenodo.10591945
title: Impact of dobutamine stress on diastolic energetic efficiency of healthy left ventricle an in vivo kinetic energy analysis

description: Riva A, Eriksson J, Viola F, Sturla F, Votta E, Ebbers T, Carlhäll CG, Dyverfeldt P. Impact of dobutamine stress on diastolic energetic efficiency of healthy left ventricle: an in vivo kinetic energy analysis. Front Cardiovasc Med. 2023 Mar 21;10:1103751. doi: 10.3389/fcvm.2023.1103751. PMID: 37025678; PMCID: PMC10071008.

Abstract



The total kinetic energy (KE) of blood can be decomposed into mean KE (MKE) and turbulent KE (TKE), which are associated with the phase-averaged fluid velocity field and the instantaneous velocity fluctuations, respectively. The aim of this study was to explore the effects of pharmacologically induced stress on MKE and TKE in the left ventricle (LV) in a cohort of healthy volunteers. 4D Flow MRI data were acquired in eleven subjects at rest and after dobutamine infusion, at a heart rate that was ∼60% higher than the one in rest conditions. MKE and TKE were computed as volume integrals over the whole LV and as data mapped to functional LV flow components, i.e., direct flow, retained inflow, delayed ejection flow and residual volume. Diastolic MKE and TKE increased under stress, in particular at peak early filling and peak atrial contraction. Augmented LV inotropy and cardiac frequency also caused an increase in direct flow and retained inflow MKE and TKE. However, the TKE/KE ratio remained comparable between rest and stress conditions, suggesting that LV intracavitary fluid dynamics can adapt to stress conditions without altering the TKE to KE balance of the normal left ventricle at rest.
DOI: 10.5281/zenodo.10591946
title: Impact of dobutamine stress on diastolic energetic efficiency of healthy left ventricle an in vivo kinetic energy analysis

description: Riva A, Eriksson J, Viola F, Sturla F, Votta E, Ebbers T, Carlhäll CG, Dyverfeldt P. Impact of dobutamine stress on diastolic energetic efficiency of healthy left ventricle: an in vivo kinetic energy analysis. Front Cardiovasc Med. 2023 Mar 21;10:1103751. doi: 10.3389/fcvm.2023.1103751. PMID: 37025678; PMCID: PMC10071008.

Abstract



The total kinetic energy (KE) of blood can be decomposed into mean KE (MKE) and turbulent KE (TKE), which are associated with the phase-averaged fluid velocity field and the instantaneous velocity fluctuations, respectively. The aim of this study was to explore the effects of pharmacologically induced stress on MKE and TKE in the left ventricle (LV) in a cohort of healthy volunteers. 4D Flow MRI data were acquired in eleven subjects at rest and after dobutamine infusion, at a heart rate that was ∼60% higher than the one in rest conditions. MKE and TKE were computed as volume integrals over the whole LV and as data mapped to functional LV flow components, i.e., direct flow, retained inflow, delayed ejection flow and residual volume. Diastolic MKE and TKE increased under stress, in particular at peak early filling and peak atrial contraction. Augmented LV inotropy and cardiac frequency also caused an increase in direct flow and retained inflow MKE and TKE. However, the TKE/KE ratio remained comparable between rest and stress conditions, suggesting that LV intracavitary fluid dynamics can adapt to stress conditions without altering the TKE to KE balance of the normal left ventricle at rest.
DOI: 10.5281/zenodo.10592162
title: Dataset related to article: Sex distribution and classification of GBA1 variants in an Italian cohort of Parkinson's disease patients analyzed over the last seventeen years

description: Sanger sequencing (.abi) or NGS files (.vcf) showing detected positive variants.
DOI: 10.5281/zenodo.10592163
title: Dataset related to article: Sex distribution and classification of GBA1 variants in an Italian cohort of Parkinson's disease patients analyzed over the last seventeen years

description: Sanger sequencing (.abi) or NGS files (.vcf) showing detected positive variants.
DOI: 10.26255/heal.hzbj-2kyf
title: Athens road network
DOI: 10.6084/m9.figshare.25111631
title: Supplementary Material for: Association between Pre-Operative Total Prostate-Specific Antigen and Survivorship of Prostate Cancer following Radical Prostatectomy: A Systematic Review

description: <b><i>Objective:</i></b> This review aimed to systematically quantify the association between pre-operative total prostate-specific antigen (<i>t</i>PSA) and survivorship of prostate cancer (PCa). <b><i>Methods:</i></b> Data sources for the review included MEDLINE, PubMed, Cochrane Library, CINAHL, Academic Search Complete, PsycINFO, and relevant reference lists. Databases were searched from inception to June 2022. The study took place between May 2022 and March 2023. We included studies that applied a quantitative approach to examine the interaction between pre-operative PSA and survivorship of PCa. Pre-operative PSA constituted the independent variable, whereas survivorship of PCa as measured by biochemical recurrence and mortality constitute the outcome variable. A risk of bias assessment was conducted with the aid of a mixed-method appraisal tool. We employed meta-analysis to quantify the association of pre-operative PSA with biochemical recurrence and mortality and computed <i>I</i><sup>2</sup> to assess the degree of heterogeneity. <b><i>Results:</i></b> We found a positive weak association between pre-operative PSA and biochemical recurrence (hazard ratio [HR] = 1.074; 95% CI = 1.042–1.106). With a median rise in PSA (≥2 ng/mL), the likelihood for biochemical recurrence increase by approximately 7.4%. There was statistically a significant association between PSA and mortality (HR = 1.222, CI = 0.917–1.630). <b><i>Conclusions:</i></b> Biochemical recurrence associates with pre-operative PSA in an inconsistent manner. The sole use of pre-operative PSA in estimating post-prostatectomy biochemical recurrence should be discouraged. There is need for a multifactorial model which employs a prudent combination of the most important and cost-effective biomarkers in predicting post-prostatectomy biochemical recurrence.
DOI: 10.6084/m9.figshare.25111631.v1
title: Supplementary Material for: Association between Pre-Operative Total Prostate-Specific Antigen and Survivorship of Prostate Cancer following Radical Prostatectomy: A Systematic Review

description: <b><i>Objective:</i></b> This review aimed to systematically quantify the association between pre-operative total prostate-specific antigen (<i>t</i>PSA) and survivorship of prostate cancer (PCa). <b><i>Methods:</i></b> Data sources for the review included MEDLINE, PubMed, Cochrane Library, CINAHL, Academic Search Complete, PsycINFO, and relevant reference lists. Databases were searched from inception to June 2022. The study took place between May 2022 and March 2023. We included studies that applied a quantitative approach to examine the interaction between pre-operative PSA and survivorship of PCa. Pre-operative PSA constituted the independent variable, whereas survivorship of PCa as measured by biochemical recurrence and mortality constitute the outcome variable. A risk of bias assessment was conducted with the aid of a mixed-method appraisal tool. We employed meta-analysis to quantify the association of pre-operative PSA with biochemical recurrence and mortality and computed <i>I</i><sup>2</sup> to assess the degree of heterogeneity. <b><i>Results:</i></b> We found a positive weak association between pre-operative PSA and biochemical recurrence (hazard ratio [HR] = 1.074; 95% CI = 1.042–1.106). With a median rise in PSA (≥2 ng/mL), the likelihood for biochemical recurrence increase by approximately 7.4%. There was statistically a significant association between PSA and mortality (HR = 1.222, CI = 0.917–1.630). <b><i>Conclusions:</i></b> Biochemical recurrence associates with pre-operative PSA in an inconsistent manner. The sole use of pre-operative PSA in estimating post-prostatectomy biochemical recurrence should be discouraged. There is need for a multifactorial model which employs a prudent combination of the most important and cost-effective biomarkers in predicting post-prostatectomy biochemical recurrence.
DOI: 10.5281/zenodo.10581850
title: Rapid and efficient labeling by a selective organic fluorophore probe highlights heterogeneity of mycobacterial populations and persister resuscitation Dataset Figure6E

description: Abstract

Many bacteria enhance their survival by generating slow-/non-growing persister subpopulations. Persisters are stress tolerant and can reestablish populations after a stress. In mycobacterial infections, such as tuberculosis, these subpopulations necessitate prolonged antibiotic therapy, as they cause chronic, recurrent, and antibiotic-tolerant infections. These subpopulations are generally very small in size, making their molecular and physiological studies extremely challenging. Consequently, new tools that facilitate their investigation are highly needed. To characterize slow-/non-growing mycobacterial populations, we present an approach that utilizes Vybrant DiD, a lipophilic, small fluorescent organic probe, for mycobacterial labeling. Using this approach, pathogenic and non-pathogenic mycobacteria species can be detected and visualized within 5-20 minutes in a specific, sensitive and non-invasive manner. It enables accurate and direct quantification of mycobacterial replication rate in vitro under different growth conditions as well as intracellularly in murine macrophages at the population and single-cell level, providing insight into mycobacterial population heterogeneity. We determined the slow-/non-growing fraction of mycobacteria during exponential growth, which increased upon a stress, and we assessed the regrowth of antibiotic-tolerant, mycobacterial cells after antibacterial treatment. Monitoring mycobacterial resuscitation after low-oxygen-induced dormancy revealed the stochastic and heterogeneous nature of the resuscitation process. While the growth rate of resuscitated bacteria did not differ from the growth rate of untreated cells, their resuscitation time was found dependent on the duration of the applied hypoxia stress. Based on its simplicity and convenience, we anticipate that this method will be widely utilized in basic research on bacterial persistence and may also be included in applied settings, e.g. high-throughput drug characterization. (256 words)

This dataset contains the data for Figure 6E.
DOI: 10.5281/zenodo.10581851
title: Rapid and efficient labeling by a selective organic fluorophore probe highlights heterogeneity of mycobacterial populations and persister resuscitation Dataset Figure6E

description: Abstract

Many bacteria enhance their survival by generating slow-/non-growing persister subpopulations. Persisters are stress tolerant and can reestablish populations after a stress. In mycobacterial infections, such as tuberculosis, these subpopulations necessitate prolonged antibiotic therapy, as they cause chronic, recurrent, and antibiotic-tolerant infections. These subpopulations are generally very small in size, making their molecular and physiological studies extremely challenging. Consequently, new tools that facilitate their investigation are highly needed. To characterize slow-/non-growing mycobacterial populations, we present an approach that utilizes Vybrant DiD, a lipophilic, small fluorescent organic probe, for mycobacterial labeling. Using this approach, pathogenic and non-pathogenic mycobacteria species can be detected and visualized within 5-20 minutes in a specific, sensitive and non-invasive manner. It enables accurate and direct quantification of mycobacterial replication rate in vitro under different growth conditions as well as intracellularly in murine macrophages at the population and single-cell level, providing insight into mycobacterial population heterogeneity. We determined the slow-/non-growing fraction of mycobacteria during exponential growth, which increased upon a stress, and we assessed the regrowth of antibiotic-tolerant, mycobacterial cells after antibacterial treatment. Monitoring mycobacterial resuscitation after low-oxygen-induced dormancy revealed the stochastic and heterogeneous nature of the resuscitation process. While the growth rate of resuscitated bacteria did not differ from the growth rate of untreated cells, their resuscitation time was found dependent on the duration of the applied hypoxia stress. Based on its simplicity and convenience, we anticipate that this method will be widely utilized in basic research on bacterial persistence and may also be included in applied settings, e.g. high-throughput drug characterization. (256 words)

This dataset contains the data for Figure 6E.
DOI: 10.6084/m9.figshare.25111706
title: Supplementary Material for: An International Survey of Practices in the Investigation and Endoscopic Treatment of Peripheral Pulmonary Lesions amongst Interventional Bronchoscopists

description: Introduction: The investigation of peripheral pulmonary lesions (PPL) can be challenging. Several bronchoscopic modalities have been developed to reach and biopsy PPL but the level of adoption of these techniques by interventional pulmonologists (IP) is unknown. This international survey was conducted to describe current practices in PPL investigation among IP. 
Methods: This survey was sent to all members of the WABIP, CTS-PA, AABIP and the GETIF. The survey was composed of 48 questions and three clinical cases to establish a portrait of modalities used to investigate and treat PPL by IP around the world.
Results: Three hundred and twelve IP responded to the survey. Most of them practice in Europe (n = 122), North America (n = 97) and Asia (n=49). Half of responders perform more than 100 endoscopic procedures for PPL annually. General anesthesia and conscious sedation are used in similar proportions (53% and 47% respectively). Rapid On site Examination (ROSE) is used when sampling PPL by 42%. Radial EBUS (69%), fluoroscopy (55%) and electromagnetic navigation (27%) are the most widely used techniques. Most IP combine techniques (89%). Robotic bronchoscopy (15%) and cone beam CT (8%) are almost exclusively used in the United States of America where, respectively, 60% and 37% of respondents reported using these modalities. Ten percent of IP currently had access to endoscopic treatment modalities for PPL. However, half of the remaining IP plan to acquire an endoscopic treatment modality in the next 2 years.
Conclusion: Available techniques and practices worldwide vary significantly regarding PPL investigation and treatment.
DOI: 10.6084/m9.figshare.25103003
title: DLBCL transcriptomics data

description: Transcriptomics dataset of 344 formalin-fixed paraffin-embedded (FFPE) tissue samples from patients with Diffuse large B-cell lymphoma (DLBCL). Gene Expression profiles of 145 target genes was done using the NanoString nCounter technology (NanoString Technologies, Seattle, WA). For details see:Staiger, A.M., Altenbuchinger, M., Ziepert, M. <i>et al.</i> A novel lymphoma-associated macrophage interaction signature (LAMIS) provides robust risk prognostication in diffuse large B-cell lymphoma clinical trial cohorts of the DSHNHL. <i>Leukemia</i> <b>34</b>, 543–552 (2020). https://doi.org/10.1038/s41375-019-0573-y
DOI: 10.6084/m9.figshare.25103003.v1
title: DLBCL transcriptomics data

description: Transcriptomics dataset of 344 formalin-fixed paraffin-embedded (FFPE) tissue samples from patients with Diffuse large B-cell lymphoma (DLBCL). Gene Expression profiles of 145 target genes was done using the NanoString nCounter technology (NanoString Technologies, Seattle, WA). For details see:Staiger, A.M., Altenbuchinger, M., Ziepert, M. <i>et al.</i> A novel lymphoma-associated macrophage interaction signature (LAMIS) provides robust risk prognostication in diffuse large B-cell lymphoma clinical trial cohorts of the DSHNHL. <i>Leukemia</i> <b>34</b>, 543–552 (2020). https://doi.org/10.1038/s41375-019-0573-y
DOI: 10.4119/unibi/2956654
title: Arabidopsis thaliana methylation pattern analysis based on ONT sequence reads

description: We sequenced the genomes of 14 Arabidopsis thaliana GABI-Kat T-DNA insertion lines (Col-0 background), which eluded flanking sequence tag-based attempts to fully characterize their insertion alleles, with Oxford Nanopore Technologies (ONT) long reads. Detailed information about each line, e.g. their T-DNA insertion site(s), have been described by Pucker et al. (BMC Genomics (2021) 22:599; https://doi.org/10.1186/s12864-021-07877-8). The DNA that has been sequenced is derived from a mixtures of tissues as expected for DNA extracted from young plantlets. For 11 of the datasets from these lines, we called 5mC methylation patterns with the tool Megalodon v.2.2.9 provided by ONT (https://github.com/nanoporetech/megalodon/). Results of this analysis are available per line as individual VCF files. We are sharing unfiltered output files to grant full control over the down-stream analysis steps and to accelerate the research in epigenomics. We identified between 706,254 and 1,020,654 positions per line where at least 80% of 5 or more reads support a methylation site. The following datasets are available and the file names reveal the respective GK line:
1. GK_040A12.vcf
2. GK_050B11.vcf
3. GK_082G09.vcf
4. GK_290G05.vcf
5. GK_399C06.vcf
6. GK_410B07.vcf
7. GK_430F05.vcf
8. GK_433E06.vcf
9. GK_654A12.vcf
10. GK_767D12.vcf
11. GK_909H04.vcf
DOI: 10.5281/zenodo.10103330
title: Code and data to "Climate change contribution to the 2023 autumn temperature records in Austria"

description: The dataset consists of the code and data used for the preprint "Climate change contribution to the 2023 autumn temperature records in Austria". 
It contains two objects:

The station data of mean monthly temperature for Vienna Hohe-Warte from 1750 to 2023 (vienna_hohe-warte.csv), which also can be downloaded here: http://www.zamg.ac.at/histalp/dataset/station/csv.php. 
The code for modeling and producing the figures of the preprint (autumn_temperature.R).