cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8034152
title: Association between preexisting lung involvements and the risk of diffuse alveolar hemorrhage in patients with microscopic polyangiitis: A multi-center retrospective cohort study

description: <b>Objectives:</b> To identify the factors associated with the risk of diffuse alveolar hemorrhage (DAH) in patients with microscopic polyangiitis (MPA), focusing on other preexisting lung involvements such as interstitial lung disease (ILD) and airway disease. <b>Methods:</b> In this retrospective cohort study, we analyzed consecutive patients with myeloperoxidase-antineutrophil cytoplasmic antibody-positive MPA who had undergone chest computed tomography (CT) before starting treatment between 2006 and 2016. Patients who already had DAH at initial CT imaging were excluded. CT images were evaluated for the presence of ILD and airway disease. The association between preexisting lung involvements and the development of DAH was assessed using logistic regression models adjusted for various clinical characteristics. <b>Results:</b> We identified 113 patients (median age 72 years; median follow-up duration 39 months), and 27 (24%) of them developed DAH during the follow-up. Airway disease was identified in 41 (36%) patients and was independently associated with the development of DAH (adjusted odds ratio 6.86, 95% confidence interval 1.85–25.4). However, ILD identified in 45 (40%) patients was not associated with DAH. <b>Conclusion:</b> Our findings suggest that DAH in MPA occurs frequently in patients with airway disease. Attention to preexisting airway disease may help predict the development of DAH.
DOI: 10.6084/m9.figshare.8034098
title: Quantitative variation in the core bacterial community associated with honey bees from <i>Varroa-</i>infested colonies

description: Infestations of the ectoparasitic mite <i>Varroa destructor</i> cause significant honey bee colony weakening, due to both host-feeding and virus transmission effects. In addition to the natural (i.e., behavioral) and innate (i.e., cellular and humoral response) mechanisms of defense against pathogens and parasites, contribution to maintain good colony health may derive from the resident microbial community. The present study investigated variation in immune-related gene expression levels and in the relative abundance of representative bacterial taxa of the core honey bee microbiota in colonies infested by <i>Varroa</i> mites in comparison with honey bees from non-infested colonies. Significant changes in the target bacterial taxa (Gammaproteobacteria, Betaproteobacteria, <i>Lactobacillus</i> spp., <i>Bifidobacterium</i> spp., <i>Brevibacillus laterosporus</i>) were detected in immune-suppressed adults emerging from <i>Varroa</i>-infested colonies. Insect stages randomly sampled from infested and non-infested hives were characterized by high variability. Emerging adults bearing sucking <i>Varroa</i> mites on their body showed a considerably higher deformed wing virus titer and a greater immune gene downregulation compared with adults without mites. Further, the abundance of the overall bacterial community and of specific bacterial taxa increased significantly in parasitized adults. A possible compensation mechanism involving the core bacterial community in <i>Varroa</i>-infested hives is discussed.
DOI: 10.6084/m9.figshare.8034134.v1
title: 1000 Genome genotype

description: The 1000 Genome genotype used in the study
DOI: 10.6084/m9.figshare.8034152.v1
title: Association between preexisting lung involvements and the risk of diffuse alveolar hemorrhage in patients with microscopic polyangiitis: A multi-center retrospective cohort study

description: <b>Objectives:</b> To identify the factors associated with the risk of diffuse alveolar hemorrhage (DAH) in patients with microscopic polyangiitis (MPA), focusing on other preexisting lung involvements such as interstitial lung disease (ILD) and airway disease. <b>Methods:</b> In this retrospective cohort study, we analyzed consecutive patients with myeloperoxidase-antineutrophil cytoplasmic antibody-positive MPA who had undergone chest computed tomography (CT) before starting treatment between 2006 and 2016. Patients who already had DAH at initial CT imaging were excluded. CT images were evaluated for the presence of ILD and airway disease. The association between preexisting lung involvements and the development of DAH was assessed using logistic regression models adjusted for various clinical characteristics. <b>Results:</b> We identified 113 patients (median age 72 years; median follow-up duration 39 months), and 27 (24%) of them developed DAH during the follow-up. Airway disease was identified in 41 (36%) patients and was independently associated with the development of DAH (adjusted odds ratio 6.86, 95% confidence interval 1.85–25.4). However, ILD identified in 45 (40%) patients was not associated with DAH. <b>Conclusion:</b> Our findings suggest that DAH in MPA occurs frequently in patients with airway disease. Attention to preexisting airway disease may help predict the development of DAH.
DOI: 10.6084/m9.figshare.8034065
title: Prevalence of coronary artery calcification and its association with mortality, cardiovascular events in patients with chronic kidney disease: a systematic review and meta-analysis

description: <b>Purpose:</b> To date, the prevalence and prognostic role of coronary artery calcification (CAC) in patients with chronic kidney disease (CKD) have been investigated in several studies, but have yielded conflicting results. The aim of this meta-analysis is to derive a more precise estimation of CAC prevalence in CKD patients and its association with cardiovascular events and mortality. <b>Methods:</b> The relevant literature was identified and evaluated from inception until July 2018 through multiple search strategies on PubMed, Embase, and Web of Science. Cross-sectional or cohort (baseline data) studies reporting CAC prevalence were included. Data extracted from eligible studies were used to calculate effect estimates (ESs) and 95% confidence intervals (95%CI). We searched databases for observational studies that explored baseline CAC and subsequent cardiovascular or all-cause mortality risk in CKD patients. <b>Results:</b> The meta-analysis included 47 studies; 38 of these were included in the final analysis of CAC prevalence. The pooled prevalence of CAC in random effect model was 60% (95%CI 53–68%). CAC was positively associated with an increased risk of all-cause mortality (hazard ratio [HR] 3.44; 95%CI 2.40–4.94), cardiovascular mortality (HR 3.87; 95%CI 2.06–7.26), and cardiovascular events (HR 2.09; 95%CI 1.19–3.67), when comparing individuals in the top CAC score group to those in the bottom CAC score group. <b>Conclusions:</b> The pooled prevalence of CAC is highly prevalent. CAC is independently associated with all-cause and cardiovascular mortality risk as well as cardiovascular events among CKD patients. In view of the high heterogeneity, larger clinical trials are still needed.
DOI: 10.6084/m9.figshare.8034098.v1
title: Quantitative variation in the core bacterial community associated with honey bees from <i>Varroa-</i>infested colonies

description: Infestations of the ectoparasitic mite <i>Varroa destructor</i> cause significant honey bee colony weakening, due to both host-feeding and virus transmission effects. In addition to the natural (i.e., behavioral) and innate (i.e., cellular and humoral response) mechanisms of defense against pathogens and parasites, contribution to maintain good colony health may derive from the resident microbial community. The present study investigated variation in immune-related gene expression levels and in the relative abundance of representative bacterial taxa of the core honey bee microbiota in colonies infested by <i>Varroa</i> mites in comparison with honey bees from non-infested colonies. Significant changes in the target bacterial taxa (Gammaproteobacteria, Betaproteobacteria, <i>Lactobacillus</i> spp., <i>Bifidobacterium</i> spp., <i>Brevibacillus laterosporus</i>) were detected in immune-suppressed adults emerging from <i>Varroa</i>-infested colonies. Insect stages randomly sampled from infested and non-infested hives were characterized by high variability. Emerging adults bearing sucking <i>Varroa</i> mites on their body showed a considerably higher deformed wing virus titer and a greater immune gene downregulation compared with adults without mites. Further, the abundance of the overall bacterial community and of specific bacterial taxa increased significantly in parasitized adults. A possible compensation mechanism involving the core bacterial community in <i>Varroa</i>-infested hives is discussed.
DOI: 10.6084/m9.figshare.8034059
title: Asthma prevalence among women aged 18 to 44 in the United States: National health and nutrition examination survey 2001–2016

description: <b>Objective:</b> To provide updated prevalence estimates of asthma and asthma medication use for women of childbearing age in the United States. <b>Methods:</b> Using data from 11,383 women aged 18–44, including a subset of 1,245 pregnant women, enrolled in the National Health and Nutrition Examination Survey (2001–2016), we assessed the age-adjusted prevalence of self-reported diagnosed asthma. For women aged 18–44, we stratified by year, demographics, and other characteristics. Furthermore, we assessed asthma medication use among women aged 18–44 with asthma. <b>Results:</b> After age-adjustment, 9.9% (95% confidence interval (CI) 9.2%, 10.7%) of women aged 18–44 and 10.9% (95% CI 7.2%, 14.6%) of pregnant women reported having asthma. Asthma prevalence was highest in 2015–2016 (12.0% 95% CI 9.8%, 14.3%) and lowest in 2003–2004 (8.6% 95% CI 6.4%, 10.8%). Women aged 18–44 with Medicaid or State Children’s Health Insurance Program insurance coverage (16.8% 95% CI 14.5%, 19.2%), obesity (14.4% 95% CI 12.9%, 15.8%), diabetes (18.7% 95% CI 12.1%, 25.2%), hypertension (16.6% 95% CI 14.2%, 19.0%), and current smokers (12.8% 95% CI 11.4%, 14.2%) had the highest asthma prevalence. Of women with asthma, 38.3% (95% CI 34.5%, 42.1%) reported using asthma medications in the past 30 days. <b>Conclusions:</b> Among women of childbearing ages, asthma burden varies across demographic and clinical characteristics and has increased in recent years.
DOI: 10.6084/m9.figshare.8034065.v1
title: Prevalence of coronary artery calcification and its association with mortality, cardiovascular events in patients with chronic kidney disease: a systematic review and meta-analysis

description: <b>Purpose:</b> To date, the prevalence and prognostic role of coronary artery calcification (CAC) in patients with chronic kidney disease (CKD) have been investigated in several studies, but have yielded conflicting results. The aim of this meta-analysis is to derive a more precise estimation of CAC prevalence in CKD patients and its association with cardiovascular events and mortality. <b>Methods:</b> The relevant literature was identified and evaluated from inception until July 2018 through multiple search strategies on PubMed, Embase, and Web of Science. Cross-sectional or cohort (baseline data) studies reporting CAC prevalence were included. Data extracted from eligible studies were used to calculate effect estimates (ESs) and 95% confidence intervals (95%CI). We searched databases for observational studies that explored baseline CAC and subsequent cardiovascular or all-cause mortality risk in CKD patients. <b>Results:</b> The meta-analysis included 47 studies; 38 of these were included in the final analysis of CAC prevalence. The pooled prevalence of CAC in random effect model was 60% (95%CI 53–68%). CAC was positively associated with an increased risk of all-cause mortality (hazard ratio [HR] 3.44; 95%CI 2.40–4.94), cardiovascular mortality (HR 3.87; 95%CI 2.06–7.26), and cardiovascular events (HR 2.09; 95%CI 1.19–3.67), when comparing individuals in the top CAC score group to those in the bottom CAC score group. <b>Conclusions:</b> The pooled prevalence of CAC is highly prevalent. CAC is independently associated with all-cause and cardiovascular mortality risk as well as cardiovascular events among CKD patients. In view of the high heterogeneity, larger clinical trials are still needed.
DOI: 10.6084/m9.figshare.8034059.v1
title: Asthma prevalence among women aged 18 to 44 in the United States: National health and nutrition examination survey 2001–2016

description: <b>Objective:</b> To provide updated prevalence estimates of asthma and asthma medication use for women of childbearing age in the United States. <b>Methods:</b> Using data from 11,383 women aged 18–44, including a subset of 1,245 pregnant women, enrolled in the National Health and Nutrition Examination Survey (2001–2016), we assessed the age-adjusted prevalence of self-reported diagnosed asthma. For women aged 18–44, we stratified by year, demographics, and other characteristics. Furthermore, we assessed asthma medication use among women aged 18–44 with asthma. <b>Results:</b> After age-adjustment, 9.9% (95% confidence interval (CI) 9.2%, 10.7%) of women aged 18–44 and 10.9% (95% CI 7.2%, 14.6%) of pregnant women reported having asthma. Asthma prevalence was highest in 2015–2016 (12.0% 95% CI 9.8%, 14.3%) and lowest in 2003–2004 (8.6% 95% CI 6.4%, 10.8%). Women aged 18–44 with Medicaid or State Children’s Health Insurance Program insurance coverage (16.8% 95% CI 14.5%, 19.2%), obesity (14.4% 95% CI 12.9%, 15.8%), diabetes (18.7% 95% CI 12.1%, 25.2%), hypertension (16.6% 95% CI 14.2%, 19.0%), and current smokers (12.8% 95% CI 11.4%, 14.2%) had the highest asthma prevalence. Of women with asthma, 38.3% (95% CI 34.5%, 42.1%) reported using asthma medications in the past 30 days. <b>Conclusions:</b> Among women of childbearing ages, asthma burden varies across demographic and clinical characteristics and has increased in recent years.
DOI: 10.5281/zenodo.4003720
title: Metadata standards and tools practice at EPFL School of Life Sciences 2020 Survey

description: In 2020, EPFL Library conducted a study about Tools and Metadata Standards practice in EPFL School of Life Sciences. By standard, we mean:<br> - terminological resources (vocabularies, terminologies, classifications, thesauri),<br> - formats and data models / schemas,<br> - structured knowledge bases (databases, reference databases, ontologies).<br> And by tools, we mean:<br> - bioinformatics software (i.e. for sequence or molecular structure analysis of proteins and genes)<br> - databases from the Life Sciences field (i.e. genome databases). Our goal was twofold: on the one hand, to gain new knowledge and insights, and on the other hand, to develop a reproducible survey methodology resolutely based on liaison librarian-data librarian collaboration. This dataset reflects the results collected during the second phase of the study: "Survey in EPFL Life Sciences Community".
DOI: 10.6084/m9.figshare.8033483
title: Basin of attraction on varying H, 2xCO2; Example of B-tipping from the on state; Example of avoided B-tipping; Example of R-tipping from the on state; Example of avoided R-tipping from Basin bifurcations, oscillatory instability and rate-induced thresholds for Atlantic meridional overturning circulation in a global oceanic box model. 29 January 2019 11 April 2019

description: Animation of Figure 7; Animation of Figure 12 red trajectory; Animation of Figure 12 black trajectory; Animation of Figure 14 red trajectory; Animation of Figure 14 black trajectory
DOI: 10.5281/zenodo.4003719
title: Metadata standards and tools practice at EPFL School of Life Sciences 2020 Survey

description: In 2020, EPFL Library conducted a study about Tools and Metadata Standards practice in EPFL School of Life Sciences. By standard, we mean:<br> - terminological resources (vocabularies, terminologies, classifications, thesauri),<br> - formats and data models / schemas,<br> - structured knowledge bases (databases, reference databases, ontologies).<br> And by tools, we mean:<br> - bioinformatics software (i.e. for sequence or molecular structure analysis of proteins and genes)<br> - databases from the Life Sciences field (i.e. genome databases). Our goal was twofold: on the one hand, to gain new knowledge and insights, and on the other hand, to develop a reproducible survey methodology resolutely based on liaison librarian-data librarian collaboration. This dataset reflects the results collected during the second phase of the study: "Survey in EPFL Life Sciences Community".
DOI: 10.6084/m9.figshare.8033483.v1
title: Basin of attraction on varying H, 2xCO2; Example of B-tipping from the on state; Example of avoided B-tipping; Example of R-tipping from the on state; Example of avoided R-tipping from Basin bifurcations, oscillatory instability and rate-induced thresholds for Atlantic meridional overturning circulation in a global oceanic box model. 29 January 2019 11 April 2019

description: Animation of Figure 7; Animation of Figure 12 red trajectory; Animation of Figure 12 black trajectory; Animation of Figure 14 red trajectory; Animation of Figure 14 black trajectory
DOI: 10.6084/m9.figshare.8033129
title: MOESM2 of Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

description: Additional file 2. List of TCGA tumour and non-tumour samples in 21 cancer types.
DOI: 10.6084/m9.figshare.8033132
title: Additional file 1: of A network-based approach for identifying suitable biomarkers for oral immunotherapy of food allergy

description: List of analyzed features of the CMA-model and PNA-model, including the number of animals per experiment and the analyzed parameters per model. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8033135
title: MOESM3 of Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

description: Additional file 3. Differentially expressed genes between patients separated by ClockLoss or ClockGain into 4th and 1st quartiles.
DOI: 10.6084/m9.figshare.8033132.v1
title: Additional file 1: of A network-based approach for identifying suitable biomarkers for oral immunotherapy of food allergy

description: List of analyzed features of the CMA-model and PNA-model, including the number of animals per experiment and the analyzed parameters per model. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8033126
title: MOESM1 of Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

description: Additional file 1. List of 32 circadian clock genes.
DOI: 10.6084/m9.figshare.8033135.v1
title: MOESM3 of Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

description: Additional file 3. Differentially expressed genes between patients separated by ClockLoss or ClockGain into 4th and 1st quartiles.
DOI: 10.6084/m9.figshare.8033129.v1
title: MOESM2 of Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

description: Additional file 2. List of TCGA tumour and non-tumour samples in 21 cancer types.
DOI: 10.6084/m9.figshare.8033120
title: Additional file 1: of Respiratory severity score as a predictive factor for severe bronchopulmonary dysplasia or death in extremely preterm infants

description: Raw data RSS. (XLSX 507 kb)
DOI: 10.6084/m9.figshare.8033126.v1
title: MOESM1 of Timing gone awry: distinct tumour suppressive and oncogenic roles of the circadian clock and crosstalk with hypoxia signalling in diverse malignancies

description: Additional file 1. List of 32 circadian clock genes.
DOI: 10.6084/m9.figshare.8033108
title: Additional file 8: of Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

description: Results of the dS analyses. (XLSX 1391 kb)
DOI: 10.6084/m9.figshare.8033120.v1
title: Additional file 1: of Respiratory severity score as a predictive factor for severe bronchopulmonary dysplasia or death in extremely preterm infants

description: Raw data RSS. (XLSX 507 kb)
DOI: 10.6084/m9.figshare.8033108.v1
title: Additional file 8: of Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

description: Results of the dS analyses. (XLSX 1391 kb)
DOI: 10.6084/m9.figshare.8033069
title: Additional file 3: of Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

description: Results of BLASTn analysis to assess presence and absence of genes or gene clusters for which the secondary metabolic products are known. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8033069.v1
title: Additional file 3: of Variation in secondary metabolite production potential in the Fusarium incarnatum-equiseti species complex revealed by comparative analysis of 13 genomes

description: Results of BLASTn analysis to assess presence and absence of genes or gene clusters for which the secondary metabolic products are known. (XLSX 25 kb)
DOI: 10.6084/m9.figshare.8033012
title: Additional file 4: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of genes that differentially expressed under the heat stress conditions and just detected in tolerant genotypes (Sacramento and NY-105). (XLSX 1518 kb)
DOI: 10.6084/m9.figshare.8033015
title: Additional file 5: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of genes showing genotype Ă treatment interaction. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.8033006
title: Additional file 3: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of core genes in the same order as the heatmap in Fig. 6. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.8033012.v1
title: Additional file 4: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of genes that differentially expressed under the heat stress conditions and just detected in tolerant genotypes (Sacramento and NY-105). (XLSX 1518 kb)
DOI: 10.6084/m9.figshare.8033000
title: Additional file 2: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of core genes that up- and down-regulated in all three genotypes. (XLSX 111 kb)
DOI: 10.6084/m9.figshare.8033006.v1
title: Additional file 3: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of core genes in the same order as the heatmap in Fig. 6. (XLSX 60 kb)
DOI: 10.6084/m9.figshare.8033015.v1
title: Additional file 5: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of genes showing genotype Ă treatment interaction. (XLSX 88 kb)
DOI: 10.6084/m9.figshare.8032991
title: Additional file 1: of Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships

description: List of up- and down-regulated genes under heat stress condition in each of three genotypes of common bean. (XLSX 535 kb)