cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3543554.v2
title: Down-regulation of 21A Alu RNA as a tool to boost proliferation maintaining the tissue regeneration potential of progenitor cells

description: 21A is an <i>Alu</i> non-coding (nc) RNA transcribed by RNA polymerase (pol) III. While investigating the biological role of 21A ncRNA we documented an inverse correlation between its expression level and the rate of cell proliferation. The downregulation of this ncRNA not only caused a boost in cell proliferation, but was also associated to a transient cell dedifferentiation, suggesting a possible involvement of this RNA in cell dedifferentiation/reprogramming. In this study, we explored the possibility to enhance proliferation and dedifferentiation of cells of interest, by 21A down-regulation, using a mixture of chemically modified Anti-21A RNAs. Our results confirmed the validity of this approach that allows the amplification of specific cell populations, in a controlled manner and without inducing permanent effects. In addition to induce cell proliferation, the procedure did not decrease the tissue regeneration potential of progenitor cells in two different cell systems.
DOI: 10.6084/m9.figshare.3543554.v1
title: Down-regulation of 21A <i>Alu</i> RNA as a tool to boost proliferation maintaining the tissue regeneration potential of progenitor cells

description: 21A is an <i>Alu</i> non-coding (nc) RNA transcribed by RNA polymerase (pol) III. While investigating the biological role of 21A ncRNA we documented an inverse correlation between its expression level and the rate of cell proliferation. The down-regulation of this ncRNA not only caused a boost in cell proliferation, but was also associated to a transient cell dedifferentiation, suggesting a possible involvement of this RNA in cell dedifferentiation/reprogramming. In this study, we explored the possibility to enhance proliferation and dedifferentiation of cells of interest, by 21A down-regulation, using a mixture of chemically modified Anti-21A RNAs. Our results confirmed the validity of this approach that could allow the amplification of specific cell populations, in a controlled manner and without inducing permanent effects. In addition to induce cell proliferation, the procedure did not decrease the tissue regeneration potential of progenitor cells in two different cell systems.
DOI: 10.6084/m9.figshare.3543551
title: Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition

description: Epigenome-wide association studies of prenatal exposure to different environmental factors are becoming increasingly common. These studies are usually performed in umbilical cord blood. Since blood comprises multiple cell types with specific DNA methylation patterns, confounding caused by cellular heterogeneity is a major concern. This can be adjusted for using reference data consisting of DNA methylation signatures in cell types isolated from blood. However, the most commonly used reference data set is based on blood samples from adult males and is not representative of the cell type composition in neonatal cord blood. The aim of this study was to generate a reference data set from cord blood to enable correct adjustment of the cell type composition in samples collected at birth. The purity of the isolated cell types was very high for all samples (&gt;97.1%), and clustering analyses showed distinct grouping of the cell types according to hematopoietic lineage. We explored whether this cord blood and the adult peripheral blood reference data sets impact the estimation of cell type composition in cord blood samples from an independent birth cohort (MoBa, n = 1092). This revealed significant differences for all cell types. Importantly, comparison of the cell type estimates against matched cell counts both in the cord blood reference samples (n = 11) and in another independent birth cohort (Generation R, n = 195), demonstrated moderate to high correlation of the data. This is the first cord blood reference data set with a comprehensive examination of the downstream application of the data through validation of estimated cell types against matched cell counts.
DOI: 10.6084/m9.figshare.3543551.v2
title: Cell type specific DNA methylation in cord blood: A 450K-reference data set and cell count-based validation of estimated cell type composition

description: Epigenome-wide association studies of prenatal exposure to different environmental factors are becoming increasingly common. These studies are usually performed in umbilical cord blood. Since blood comprises multiple cell types with specific DNA methylation patterns, confounding caused by cellular heterogeneity is a major concern. This can be adjusted for using reference data consisting of DNA methylation signatures in cell types isolated from blood. However, the most commonly used reference data set is based on blood samples from adult males and is not representative of the cell type composition in neonatal cord blood. The aim of this study was to generate a reference data set from cord blood to enable correct adjustment of the cell type composition in samples collected at birth. The purity of the isolated cell types was very high for all samples (&gt;97.1%), and clustering analyses showed distinct grouping of the cell types according to hematopoietic lineage. We explored whether this cord blood and the adult peripheral blood reference data sets impact the estimation of cell type composition in cord blood samples from an independent birth cohort (MoBa, n = 1092). This revealed significant differences for all cell types. Importantly, comparison of the cell type estimates against matched cell counts both in the cord blood reference samples (n = 11) and in another independent birth cohort (Generation R, n = 195), demonstrated moderate to high correlation of the data. This is the first cord blood reference data set with a comprehensive examination of the downstream application of the data through validation of estimated cell types against matched cell counts.
DOI: 10.6084/m9.figshare.3543551.v1
title: Cell type specific DNA methylation in cord blood: a 450K-reference data set and cell count-based validation of estimated cell type composition

description: Epigenome-wide association studies of prenatal exposure to different environmental factors are becoming increasingly common. These studies are usually performed in umbilical cord blood. Since blood comprises multiple cell types with specific DNA methylation patterns, confounding caused by cellular heterogeneity is a major concern. This can be adjusted for using reference data consisting of DNA methylation signatures in cell types isolated from blood. However, the most commonly used reference data set is based on blood samples from adult males and is not representative of the cell type composition in neonatal cord blood. The aim of this study was to generate a reference data set from cord blood to enable correct adjustment of the cell type composition in samples collected at birth. The purity of the isolated cell types was very high for all samples (&gt;97.1%), and clustering analyses showed distinct grouping of the cell types according to hematopoietic lineage. We explored whether this cord blood and the adult peripheral blood reference data sets impact the estimation of cell type composition in cord blood samples from an independent birth cohort (MoBa, n = 1092). This revealed significant differences for all cell types. Importantly, comparison of the cell type estimates against matched cell counts both in the cord blood reference samples (n = 11) and in another independent birth cohort (Generation R, n = 195), demonstrated moderate to high correlation of the data. This is the first cord blood reference data set with a comprehensive examination of the downstream application of the data through validation of estimated cell types against matched cell counts.
DOI: 10.6084/m9.figshare.3543548
title: The translation factors of <i>Drosophila melanogaster</i>

description: Synthesis of polypeptides from mRNA (translation) is a fundamental cellular process that is coordinated and catalyzed by a set of canonical ‘translation factors’. Surprisingly, the translation factors of <i>Drosophila melanogaster</i> have not yet been systematically identified, leading to inconsistencies in their nomenclature and shortcomings in functional (Gene Ontology, GO) annotations. Here, we describe the complete set of translation factors in <i>D. melanogaster</i>, applying nomenclature already in widespread use in other species, and revising their functional annotation. The collection comprises 43 initiation factors, 12 elongation factors, 3 release factors and 6 recycling factors, totaling 64 of which 55 are cytoplasmic and 9 are mitochondrial. We also provide an overview of notable findings and particular insights derived from <i>Drosophila</i> about these factors. This catalog, together with the incorporation of the improved nomenclature and GO annotation into FlyBase, will greatly facilitate access to information about the functional roles of these important proteins.
DOI: 10.6084/m9.figshare.3543548.v2
title: The translation factors of <i>Drosophila melanogaster</i>

description: Synthesis of polypeptides from mRNA (translation) is a fundamental cellular process that is coordinated and catalyzed by a set of canonical ‘translation factors’. Surprisingly, the translation factors of <i>Drosophila melanogaster</i> have not yet been systematically identified, leading to inconsistencies in their nomenclature and shortcomings in functional (Gene Ontology, GO) annotations. Here, we describe the complete set of translation factors in <i>D. melanogaster</i>, applying nomenclature already in widespread use in other species, and revising their functional annotation. The collection comprises 43 initiation factors, 12 elongation factors, 3 release factors and 6 recycling factors, totaling 64 of which 55 are cytoplasmic and 9 are mitochondrial. We also provide an overview of notable findings and particular insights derived from <i>Drosophila</i> about these factors. This catalog, together with the incorporation of the improved nomenclature and GO annotation into FlyBase, will greatly facilitate access to information about the functional roles of these important proteins.
DOI: 10.6084/m9.figshare.3543548.v1
title: The Translation Factors of <i>Drosophila melanogaster</i>

description: Synthesis of polypeptides from mRNA (translation) is a fundamental cellular process that is coordinated and catalyzed by a set of canonical ‘translation factors’. Surprisingly, the translation factors of <i>Drosophila melanogaster</i> have not yet been systematically identified, leading to inconsistencies in their nomenclature and shortcomings in functional (Gene Ontology, GO) annotations. Here, we describe the complete set of translation factors in <i>D. melanogaster</i>, applying nomenclature already in widespread use in other species, and revising their functional annotation. The collection comprises 43 initiation factors, 12 elongation factors, 3 release factors and 6 recycling factors, totaling 64 of which 55 are cytoplasmic and 9 are mitochondrial. We also provide an overview of notable findings and particular insights derived from <i>Drosophila</i> about these factors. This catalog, together with the incorporation of the improved nomenclature and GO annotation into FlyBase, will greatly facilitate access to information about the functional roles of these important proteins.
DOI: 10.6084/m9.figshare.3543530
title: Effect of cigarette smoke on monocyte procoagulant activity: Focus on platelet-derived brain-derived neurotrophic factor (BDNF)

description: Cigarette smoke (CS) activates platelets, promotes vascular dysfunction, and enhances Tissue Factor (TF) expression in blood monocytes favoring pro-thrombotic states. Brain-derived neurotrophic factor (BDNF), a member of the family of neurotrophins involved in survival, growth, and maturation of neurons, is released by activated platelets (APLTs) and plays a role in the cardiovascular system. The effect of CS on circulating levels of BDNF is controversial and the function of circulating BDNF in atherothrombosis is not fully understood. Here, we have shown that human platelets, treated with an aqueous extract of CS (CSE), released BDNF in a dose-dependent manner. In addition, incubation of human monocytes with BDNF or with the supernatant of platelets activated with CSE increased TF activity by a Tropomyosin receptor kinase B (TrkB)-dependent mechanism. Finally, comparing serum and plasma samples of 12 male never smokers (NS) and 29 male active smokers (AS) we observed a significant increase in microparticle-associated TF activity (MP-TF) as well as BDNF in AS, while in serum, BDNF behaved oppositely. Taken together these findings suggest that platelet-derived BDNF is involved in the regulation of TF activity and that CS plays a role in this pathway by favoring a pro-atherothrombotic state.
DOI: 10.6084/m9.figshare.3543530.v1
title: Effect of cigarette smoke on monocyte procoagulant activity: Focus on platelet-derived brain-derived neurotrophic factor (BDNF)

description: Cigarette smoke (CS) activates platelets, promotes vascular dysfunction, and enhances Tissue Factor (TF) expression in blood monocytes favoring pro-thrombotic states. Brain-derived neurotrophic factor (BDNF), a member of the family of neurotrophins involved in survival, growth, and maturation of neurons, is released by activated platelets (APLTs) and plays a role in the cardiovascular system. The effect of CS on circulating levels of BDNF is controversial and the function of circulating BDNF in atherothrombosis is not fully understood. Here, we have shown that human platelets, treated with an aqueous extract of CS (CSE), released BDNF in a dose-dependent manner. In addition, incubation of human monocytes with BDNF or with the supernatant of platelets activated with CSE increased TF activity by a Tropomyosin receptor kinase B (TrkB)-dependent mechanism. Finally, comparing serum and plasma samples of 12 male never smokers (NS) and 29 male active smokers (AS) we observed a significant increase in microparticle-associated TF activity (MP-TF) as well as BDNF in AS, while in serum, BDNF behaved oppositely. Taken together these findings suggest that platelet-derived BDNF is involved in the regulation of TF activity and that CS plays a role in this pathway by favoring a pro-atherothrombotic state.
DOI: 10.6084/m9.figshare.3543503
title: Launching awareness: causal events enter awareness faster than non-causal events

description: These are the raw data accompanying the following paper: <br>Moors, P., Wagemans, J., de-Wit, L. (2017). Launching awareness: causal events enter awareness faster than non-causal events. PeerJ.
DOI: 10.6084/m9.figshare.3543503.v1
title: Launching awareness: causal events enter awareness faster than non-causal events

description: These are the raw data accompanying the following paper: <br>Moors, P., Wagemans, J., de-Wit, L. (2017). Launching awareness: causal events enter awareness faster than non-causal events. PeerJ.
DOI: 10.6084/m9.figshare.3543491
title: Toward Automatic Model Comparison: An Adaptive Sequential Monte Carlo Approach

description: Model comparison for the purposes of selection, averaging, and validation is a problem found throughout statistics. Within the Bayesian paradigm, these problems all require the calculation of the posterior probabilities of models within a particular class. Substantial progress has been made in recent years, but difficulties remain in the implementation of existing schemes. This article presents adaptive sequential Monte Carlo (SMC) sampling strategies to characterize the posterior distribution of a collection of models, as well as the parameters of those models. Both a simple product estimator and a combination of SMC and a path sampling estimator are considered and existing theoretical results are extended to include the path sampling variant. A novel approach to the automatic specification of distributions within SMC algorithms is presented and shown to outperform the state of the art in this area. The performance of the proposed strategies is demonstrated via an extensive empirical study. Comparisons with state-of-the-art algorithms show that the proposed algorithms are always competitive, and often substantially superior to alternative techniques, at equal computational cost and considerably less application-specific implementation effort. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3543491.v1
title: Toward Automatic Model Comparison: An Adaptive Sequential Monte Carlo Approach

description: Model comparison for the purposes of selection, averaging, and validation is a problem found throughout statistics. Within the Bayesian paradigm, these problems all require the calculation of the posterior probabilities of models within a particular class. Substantial progress has been made in recent years, but difficulties remain in the implementation of existing schemes. This article presents adaptive sequential Monte Carlo (SMC) sampling strategies to characterize the posterior distribution of a collection of models, as well as the parameters of those models. Both a simple product estimator and a combination of SMC and a path sampling estimator are considered and existing theoretical results are extended to include the path sampling variant. A novel approach to the automatic specification of distributions within SMC algorithms is presented and shown to outperform the state of the art in this area. The performance of the proposed strategies is demonstrated via an extensive empirical study. Comparisons with state-of-the-art algorithms show that the proposed algorithms are always competitive, and often substantially superior to alternative techniques, at equal computational cost and considerably less application-specific implementation effort. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.3543467
title: Spike, burst and network spike data files generated using the IGM.MEA analysis package in the mature culture experiment in which the sponge was added on DIV19 (Sup Fig S8).

description: Files in this zip folder are those generated after spikelist files were run through the analysis pipeline. These files are those used to generate Supplemental Figure S8.
DOI: 10.6084/m9.figshare.3543467.v2
title: Spike, burst and network spike data files generated using the IGM.MEA analysis package in the mature culture experiment in which the sponge was added on DIV19 (Sup Fig S8).

description: Files in this zip folder are those generated after spikelist files were run through the analysis pipeline. These files are those used to generate Supplemental Figure S8.
DOI: 10.6084/m9.figshare.3543467.v1
title: Data Files Associated with Mature Culture Experiment (DIV19)

description: Files in this zip folder are those generated after spikelist files were run through the analysis pipeline. These files are those used to generate Supplemental Figure S8.
DOI: 10.6084/m9.figshare.3543305.v1
title: Real world evidence of use of anti-VEGF therapy in Denmark

description: <b>Objective:</b> This study evaluates real-world evidence regarding the frequency of anti-vascular-endothelial-growth-factor (VEGF) injections during the first year of therapy of treatment-naïve patients with neovascular age-related macular degeneration (nAMD), diabetic macular edema (DME) and retinal vein occlusion (RVO) from the Danish National Patient Registry. There was a switch in anti-VEGF treatment for naïve nAMD patients during the study period, following the introduction of aflibercept, which was expected to reduce the injection frequency relative to ranibizumab due to a perception of prolonged treatment duration of aflibercept. <b>Methods:</b> All treatment-naïve nAMD, DME or RVO patients who received an intravitreal injection in Denmark from 1 January 2012 to 31 July 2015 were eligible for inclusion. Patients were required to have been treated for at least one year and, for nAMD, to have received at least three injections during the first four months of treatment. Patients were allocated to half-year groupings (2012/1 to 2014/1) based on registration of their first intravitreal injection. Injection frequency during the first year of treatment was calculated for each group and <i>t</i>-tests investigated whether injection frequencies changed over time. <b>Results:</b> In treatment naïve nAMD patients (<i>n</i> = 500), the mean (SD) number of anti-VEGF injections increased significantly from 6.04 (1.71) in 2012/1 to 6.73 (1.62) in 2014/1 (<i>p</i> = .001; 2012/1 and 2012/2 vs. 2014/1) across all treatments. A similar trend was found for DME patients (<i>n</i> = 76) from 2012/1 to 2014/1 and RVO patients (<i>n</i> = 82) from 2012/2 to 2014/1, with mean injection frequencies increasing significantly from 5.14 (2.29) to 5.93 (1.98) (<i>p</i> = .007), and from 4.83 (1.21) to 6.08 (1.55) (<i>p</i> = .024), respectively. <i>Post hoc</i> sensitivity analysis also found a significant increase in injection frequency in nAMD patients who did not receive a loading phase (4.55 in 2012/1 and 5.05 in 2014/1; <i>p</i> = .006; <i>n</i> = 616). <b>Conclusions:</b> In contrast to the decrease in injection frequency predicted with a switch to aflibercept treatment for nAMD, our study showed that injection frequencies increased significantly from 2012 to 2014 in patients initiating therapy across the three diseases.
DOI: 10.6084/m9.figshare.3543296
title: READme FIRST - Metadata Description

description: This Document will help guide you through the flow of documentation and code in this project.
DOI: 10.6084/m9.figshare.3543296.v1
title: READme FIRST - Metadata Description

description: This Document will help guide you through the flow of documentation and code in this project.
DOI: 10.6084/m9.figshare.3543293
title: A tale of two paralogs: human Transformer2 proteins with differential RNA-binding affinities

description: The Transformer2 (Tra2) proteins in humans are homologues of the <i>Drosophila</i> Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. Here, we provide a structural basis for this genetic backup circuit, using molecular modelling and dynamics studies. We show that the two proteins display similar binding specificities, but differential affinities to a short GAA-rich RNA stretch. Starting from the 6-nucleotide RNA in the solution structure, close to 4000 virtual mutations were modelled on RNA and the domain–RNA interactions were studied after energy minimisation to convergence. Separately, another known 13-nucleotide stretch was docked and the domain–RNA interactions were observed through a 100-ns dynamics trajectory. We have also demonstrated the ‘compensatory’ mechanism at the level of domains in one of the domain repeat-containing RNA-binding proteins.